Puella Magi Madoka Magica/WMG/2

"Deny the obvious. Uphold the inane."

The page has grown big enough to start corrupting the wiki software. Confirmed and Jossed theories are here. Crossover and Meta theories are here.

Unconfirmed (for now)
Stuff that we haven't gotten an answer to yet, but may possibly get an answer to in the future.

The same traffic accident that killed Mami's parents injured Kamijou.
Like Mami said, her parents were killed in an accident. We don't know when this was, so it's possible Kamijou was hurt in the same accident. Unfortunately, Mami got the worse end of it.
 * from Kazumi Magica may have also been involved in the same accident. Asunaro and Mikitihara may not be that far apart.

Kyubei knows jack about the Law of Conservation of Energy.
Which means that what he's doing is because he doesn't have the slight idea to where the dispersed energy from the Universe's heating is going. It means that it's being recycled, somehow. Perhaps into human emotions, perhaps into something else.

Homura's time travel is what's causing the Universe's energy problems.
Because such a powerful ability might have taking energy not only from Homura herself, but from somewhere else. Which means that in the end, Kyubei caused exactly what he seemed to be trying to prevent.

Post-Ending Homura is a Multiverse Composite Being.
Like Madoka; Homura's time travel shenanigans tied her existence to that of the Dharma of all her Alternate Universe selves.
 * Even with Madoka's wish; this didn't end. After all, Madoka's wish covered "every world."
 * ALL previous Magical Girl Homuras also received Madoka's ribbon in every timeline; tying them to each other (and Homura to herselves). Each one remembers every previous (and later) timelines as well.
 * For sanity's sake; when dealing with other humans; Homura keeps her perception and memories to the reality she's in at the time (thus she's a bit lonely when in "the real world"); but when gametime is on against Demons; she draws on the entire collective of every Homura. That's why Dark Angel Homura is so strong; she's all of the Homuras. It's also why Dark Angel Homura is smiling. She's quite alien by human standards; but it's okay. She's not alone; she's fighting for the world her goddess loves; and they will be reunited. One day. (And what's time? She's ancient.)
 * She's basically what would happen if Rika and Bernkastel had fused and took it a lot better.

The perpetual existence of the Universe that the Incubators want would be a horror beyond imagining.
Entropy; death; is ultimately a necessary function to the Universe. Keep in mind, the Incubators have zero concept of quality of life. As long as something continues to exist; in any form; they see it as their job accomplished. An endless, eternal And I Must Scream.


 * Also the same reason the the Anti-Spirals justifying themselves with preserving the universe is seen by spirals as jack shit.
 * The Kyubey are to the universe what Franken Fran is to a single human life. Sweet dreams!

Homura was given filler backstory for her existence and knowledge in the new timeline.
In order to prevent Time Paradox; Homura was given new backstory (her previous memory wasn't erased; she remembers the "official" timeline like a dream, her memory of her constant timelines cannot be muted.) All her life, she dreamed of a girl. Madoka. She knew that this girl was the focus of her entire existence, but she didn't know why. Along comes Incubator. Homura's wish was to know what's this missing "something" in her heart. She wished to know what and who this hole was. Her Mahou Shoujo form came with that bow and ribbon.
 * Kyubey thinks Homura is bonkers; wishing for a dream memory to be filled doesn't make it true. But she's very strong so he goes along with this "I was a Magical Girl from a previous timeline" story because it's not disruptive. (The Kyubey would be far more curious if Homura was a magical girl who had NO RECORD of the Incubators ever turning her into one.)

Homura's Black Wings were simply her Attack Reflector power while in The Corruption.
Word of God says that her wings deflect attacks against her. The Barren Landscape of the Demons is a Fisher Kingdom that corrupts anyone in it, a general continuous attack. What we're seeing is simply the miasmic evil reflecting off her. Her wings are white when she's in a relatively clean area.

Homura is immortal and will never be reunited with Madoka.
It's the kind of sting-in-the-butt Urobu likes. Homura at the very end is seen being surrounded by the "witchy" wings. It's all the despair she feels coming to claim her. But every time Homura starts to fall to despair, she will feel hope that she will be with Madoka, that gives her hope and/or happiness of finally seeing her beloved again. And because of the "Hope and despair always balance out to zero" law that trumps even Thermodynamics, that happiness will drive away the complete "boot on the face forever" that is needed to call Madoka to get her. That explains why, in the end, she was followed by the darkness. In short, she will never see Madoka again, until she realizes that she will never see her again. Alas, poor Homu-chan!
 * It's jossed in the manga, but the anime...
 * Rather, she will not be able to use the "normal" route. She will have to either have to complete her Dharma of protecting the world Madoka loves by taking the Long Path to godhood; or else die doing so. (She's not going to be killed easily, though.)

There was no actual Cosmic Retcon. Goddess/Jesus Madoka is actually Kriemhild Gretchen, and the new universe is, or inside a witch sphere.
It just happens that she assimilated the entire universe in her barrier. Madoka had been so powerful that her witch sphere contains the whole material world. Though whether the laws of entropy are the same is unknown. A worse possibility is that Demons does not produce real entropy, just maintaining the "show" for Madoka.
 * An interesting theory, but it doesn't seem to fit with the description of Kriemhild Gretchen who is stated to be somewhat of a Lotus Eater Machine. Earth in the ending is certainly not a paradise, Madoka only made life slightly easier for Magical Girls.

Mami's wish gave her larger breasts.
No, she didn't intentionally wish for those; that was a side effect. Whatever the wording of her wish, it resulted in her not dying and having a healthier and more developed body.

Kyuubey tells people different things about his origin.
He tells some contractees that he's an alien. He tells others that he's an angel/demon. Others he refers to himself as a fairy. He has a different origin story for whoever asks.
 * Why so serious?
 * Considering that the girls in Puella Magi Kazumi Magica have referred to the Incubators as fairies...

Witches' dimensions are some sort of Ironic Hell

 * Seeing the witch cards.

Walpurgis Night is of extraterrestrial origin

 * Similar to Madoka in timeline 4. Walpurgis is a magical girl strong enough to destroy her own homeworld. She has moved since to do the same here.
 * Perhaps not extraterrestrial, but could be a magical girl from another country (which would be very powerful, but not enough to destroy a planet, allowing Madoka to be more powerful than she is; the girls didn't know said country was destroyed by a witch because they didn't know what a witch was at the time this happened. Might be Too Soon to theorize this sort of thing, taking in consideration the wake of recent catastrophies worldwide, but might be very plausible (that could be the reason they preferred to keep the broadcast on hold, to not affect sensibilities).

Kyubey granted Homura's wish because he wants to increase Madoka's power

 * I think it is quite possible. That becase Kyuube didn't meet his energy goal. He granted Homura's wish in order for him to somehow increase Madoka's power and get more power from her. This would explain why Madoka seems to be getting stronger after each timeline. Of course, as we say, Hoist by His Own Petard.
 * Madoka is absorbing Homura's grief, which is renewed with each reset.
 * The fact that it increases her power is confirmed, Kyubey's intent unknown.
 * It seems unlikely; Kyubee didn't seem to like Madoka's wish, tried to talk her out of it, and granted it anyway. One gets the impression that as far as he's concerned, the contract is already signed, and just waiting for the wish to go into effect.

Boys aren't as suitable as girls for energy generation, hence the reason they only use girls

 * This being a deconstruction. There must be a reason plot-wise. Boys aren't offered the same thing as girls.
 * Wasn't this confirmed? Kyubey stated that human females "in their second growth phase" were the most emotional creatures in the universe (paraphrased), and therefore the most useful to him. He wouldn't have any use of Puerorum Magi (Magical Boys).

Kyubee is able to lie and in fact already has

 * Remeber that in episode 9 he said to Madoka that . Well in episode 10 he said . This means that he is able to lie.
 * "Humanity could join my species one day, don't you want the universe to still be around?" isn't turned into lying by "well, fulfilled my quota, fuck these guys". All he told Madoka was that humanity could become that advanced and that it would be in her interest to help contribute her energy. That doesn't mean he actually ever cared about humanity. And he didn't know in the fourth timeline that Madoka would be that powerful. You can't fairly compare statements from two different timelines.
 * Not nesesarily. He used the argument of "humans may join us if you become a puella magi!" in timeline 5. Despite the fact that he knows that Madoka will become a witch strong enough to destroy this world.
 * So? There's still no contradiction between his statements, just his usual omission of relevant facts. His initial offering was always an assertion of *possibility*:'Humanity COULD join us....' What Kyubey failed to mention was the *prob*ability of that statement being realized (i.e. near zero).
 * First of all, if someone tells you that they can't lie, take the possibility of Blatant Lies first. Also, Kyubey would rather prefer Jedi Truth because a modified truth is more believable and has more supporting evidence than a lie made from the ground up.

The reason why Madoka has so much power is because
Scenario: Madoka becomes a magical girl. Homura.

but events play out mostly the same. Eventually, though, Kyuubey notices how much power Madoka has and begins focusing much of his time getting her to contract with him, which pushes Homura further to. However, she misses the entire point of what.

Bonus points if Madoka. Or maybe I'm just wishing TTGL-style optimism comes into play.


 * About the relation between Madoka and

Kyubey is trying to hatch a higher being, similar to a god
In episode 9, we find out that Kyubey However, as the universe is constantly losing energy, this strikes a parallel with  However, I am sure that Kyubey knows this, and is only using that as an excuse to hide his true intentions, this being Kyubey after all. His real intention is given away by His real plan is to  He is trying so hard to get Madoka because  would probably be enough to hatch the being.
 * Or worse, he might have discovered that.

Kyuubey is a Literal Genie.

 * Actually, it seems to be worse. He actually grants the wish they desire, and it destroys them more completely than a mere Literal Genie ever could.

Kyubey is evil.
Or at least has less than good motives. Look at him. He looks as cute as a button, but he has to speak telepathically. Thus, his face is always stuck in that permanent smile. This is very good for hiding any other emotions that he might have in the future. Gen Urobuchi has already semi-Jossed a lot of these theories; he's written on his Twitter account that he's seen far too many people jumping to conclusions about Kyubey and refusing to trust him, when that wasn't the creators' intention. Just because Kyubey, unlike most mahou-shoujo mascots, has creepy eyes and talks through telepathy doesn't make him automatically evil. Of course, this doesn't exclude the possibility that Urobuchi's lying his ass off. Note that in Episode 1, when Kyubey was running away from Homura, he was covered in wounds—but not bleeding. Kyubey is a shell, hiding something much more sinister. Also—According to Episode 5, Kyubey creates all the magical girls, including Homura, who "uses his power but he didn't give it to her", or some such (Exact quote?).
 * There's a reason everyone considers him as a Devil figure and The Deceiver.
 * This thing gives me the vibes of Dung Beetle.
 * Note that Kyubey and Mami very intentionally make sure that Homura never gets a chance to speak extensively with Madoka... even in safe places like at school.
 * Considering that there are numerous quotes of Gothe's Faust in the second episode, this is actually not very far-fetched. Both works are about someone being approached by a cute animal which offers them a wish. The dog in Faust is the devil.
 * Note that Homura pauses and refuses to answer when asked about her wish—leading credence to the idea that the "wish" stuff is a lie made up by Kyubey to tempt Madoka.
 * It's heavily insinuated that the "Making a Selfless Wish is a BAD IDEA" thing is referring to Homura, who may have made a wish on someone else's behalf only for it to not work out.
 * Observe episode 3, where in a flashback you can see Mami dying in a car wreck, with Kyubey happily jumping in to make her an offer she can't refuse.
 * This happens again in episode 4. Kyubey shows up in front of Sayaka at just the moment Kamijou is at a high point of despair over his illness.
 * Episode three has made me believe he's lying his ass off.
 * On the other hand, the implications of Kyubey's evilness are so obvious it could be a Red Herring.
 * Observe in Episode 5 when we see Kyubey empower Sayaka—he reaches into her and rips out her soul in order to make a gem out of it.
 * It's getting kind of ridiculous as of episode 6, when we find out that  He couldn't be any more obvious, even if he started dancing around yelling "I'M EVIL!".
 * In Episode 7, Homura supports the idea that Kyubey isn't exactly evil. Rather, he has no concept of human morality and values. Whether or not this amounts to the same thing is up to you for now.
 * So....episode 8
 * Not necessarily. He could be a third, neutral faction, like a natural (for the setting) force. Having said that, hell yes, he's evil.
 * In episode 9, Kyubey explains his motivations, or at least what he claims his motivations are. Even assuming that he told the whole story (most likely not a safe assumption), it still means that at best he is essentially an Anti-Spiral.
 * On that note...
 * Episode 10 makes it worse. In episode 9, Kyuubey said . In episode 10?   In other words, what he said was basically Blatant Lies.  . Definitely Lawful Evil.
 * I'll echo one of the other WMG comments;

Kyubey, in addition to being the obvious, is also a Koschei

 * As quoted: "Koschei cannot be killed by conventional means targeting his body. His soul is hidden separate from his body inside a needle, which is in an egg, which is in a duck, which is in a hare, which is in an iron chest (sometimes the chest is crystal and/or gold), which is buried under a green oak tree, which is on the island of Buyan, in the ocean. As long as his soul is safe, he cannot die. If the chest is dug up and opened, the hare will bolt away. If it is killed, the duck will emerge and try to fly off. Anyone possessing the egg has Koschei in their power. He begins to weaken, becomes sick and immediately loses the use of his magic. If the egg is tossed about, he likewise is flung around against his will. If the egg or needle is broken (in some tales this must be done by specifically breaking it against Koschei's forehead), Koschei will die."

So Homura could legitimately kill that damned thing if she finds the right duck...the day is saved.

It was all part of Kyubey's plan for

 * Another reason that supports this theory is how in Episode 9 Kyubey deliberately manipulates to sacrifice herself, eliminating all the other Puella Magi and coercing Homura into a Xanatos Gambit: try and fight Walpurgis alone and lose, or have Madoka make a contract with Kyubey to help her win.
 * This theory doesn't make any sense, because, Madoka would have made a contract with Kyubey right there and then.
 * ...But it is possible that Charlotte and her world were warping the minds of Madoka and Mami at that time. I highly doubt it was a coincidence that they were talking about wishing for a cake inside of the world of a cake-obsessed witch, which meant that Madoka would had probably changed her mind once she left Charlotte's dimension and her mind was cleared of any external influences. Besides, don't pretend that we know Madoka better than Kyubey does, he stares into her soul after all. In fact, I starting to believe that...

Kyubey is responsible for every major event that has happened in the show so far.
This includes everything, and I mean everything, that has happened from episode 3 onwards.

However, in order to do this, he probably needed some kind of mind warping powers, and he may very well have them, but said powers probably only work on "normals" such as Kyousuke (possibly used in episode 4, ), Junko (possibly used in episode 6, ) and Hitomi (possibly used in episode 7 ). However, that, combined with his mind reading of the mahou shoujo, is more than for him to influence everything that has happened so far. I'm not talking full-blown mind control, by the way, I'm thinking it's more along the lines of a subconscious voice which is egging the characters to say certain things.
 * I'm really hoping he didn't plan Episode 12. I really hope.

Mami's wish was
Kyubey just fulfilled it in the bluntest way possible after she befriended Madoka.
 * ;_;
 * Unlikely given that in another timeline she was with Sayaka, Homura, and Madoka, and certainly still alive.
 * It's certainly possible to be around other people and be all alone. Although being alone with other people is better than being alone by yourself.
 * Apparently, this suggests that Kyubey is a Literal Genie.

The witch of Episode 3 wasn't evil
The monster wasn't doing anything harmful or threatening until Mami attacked it. Then it merely acted in self-defense.
 * If the information about witches it correct, it would have drained the life of people in the hospital. After observing the woman who attempted suicide in Episode 2, we can assume that this is plausible.

Walpurgisnacht is when a hell of a lot of witches will congregate to start the apocalypse.
Expect them...having the world go up in flames. That, and they influence a lot of people with their witch-kisses to go insane and destroy everything. Still with fire. After all: "In Germany, Walpurgisnacht, the night from 30 April to 1 May, is the night when witches are reputed to hold a large celebration on the Brocken and await the arrival of spring. ..... A scene in Goethe's Faust Part One is called "Walpurgisnacht", and one in Faust Part Two is called "Classical Walpurgisnacht". .....In some parts of northern coastal regions of Germany, the custom of lighting huge fires is still kept alive to celebrate the coming of May, while most parts of Germany have a derived Christianized custom around Easter called "Easter fires". In rural parts of southern Germany, it is part of popular youth culture to play pranks such as tampering with neighbours' gardens, hiding possessions, or spraying graffiti on private property. These pranks occasionally result in serious damage to property or bodily injury."


 * For those interested, in Goethe's Faust the Walpurgisnacht of Act One had Mephistopheles taking Faust to a big gathering of witches (and wizards) all singing and flying. Interestingly, there was a short piece of dialogue with a half-witch who couldn't fly, and she was told that if she can't fly on that night she'll never fly again. A half-witch...you mean like a
 * Thanks, to the above troper. Therefore, Walpurgisnacht is the event in the prologue, Madoka's the half-witch, and Kyubee is Mephistopheles. And the world will perish in a witch's bonfire while crazed humans destroy things, leading to The End of the World as We Know It.
 * The above troper was actually thinking Homura was the half-witch, and that Madoka was Faust.
 * Not directly seen, but still possible.

Human souls sporulate.

 * A weird thought I just had. Witch familiars eat people and become a witch-clone. So what if human souls do something similar? According to Kyubey human spirits are annihilated upon death...supposing they disintegrate into little pieces, each waiting for a chance to be reborn? So a human day of judgement/afterlife is less a ressurection and more like a fungal bloom. Nice, but a bit creepy IMO.

Madoka was born with two souls

 * It explains her power and the opening henshin scene.
 * Unlikely. With the unveiling of a time traveler, we may end up seeing a timeskipped future Madoka come back, however.
 * Unlikely, but not directly contradicted.

Magical girls don't age
Since their bodies are just empty shells that can be maintained by magic. This could also mean that...
 * May or may not be the reason why (Since memories are stored in the soul here, it's probably not strictly necessary for the whole body to travel through time tho) Heck, could even explain the below.

Kyouko is older than she looks

 * In the concept art showing a younger Kyouko and her family, Kyouko and her sister are wearing fairly modern clothes; however, the art is not within context. However, a shot in Episode 7 shows the younger Kyouko drawn normally; her outfit is distinctly modern, detracting from the theory that she is centuries old.
 * Doesn't mean she isn't older than she looks. For all we know, she could very well be, chronologically speaking, on her twenties, without ant major problems.
 * Jossed in the third Drama CD, in which Kyouko says she has been a magical girl for about a year when talking with Homura at a strategy meeting, and was fighting her first witch when she first met Mami.

They're all Reality Warpers, not just magic girls
Isn't this pretty obvious?

Kyubey claims he can grant any wish, but it's really a matter of letting them grant their own wishes. Kyubey himself even admits that despite developing the technology that unlocks this potential from humans (Soul Gems), the Incubators are still unable to comprehend why Puella Magi can warp reality in the first place. Homura, who attempts to be a Nanoha-style brawler and whose Time Lord powers (which arguably allows for the most creativity, just ask anyone who watched Doctor Who) are restricted by her depression and the single duty/hope to protect Madoka, is the weakest of them; it's all about imagination.

The witches are only defeated, not killed, and Kyubey is saving them for his evil plan.
Since we now know that witches are Puella Magi who absorbed too much corruption, we can infer that grief seed are just like soul gems. When a Puella Magi pours their corruption into a grief seed, they are making the witch more powerful. Once a witch is powered up enough, Kyubey stores away the grief seed for a time when he can put his plan into action. When that time comes, he will release the grief seeds and allow the witches' bodies to regenerate and use his army of witches to destroy the world.
 * His full name is Incubator, so...

An alternate to the above theory on Grief Seeds...
The Incubator consolidates the corruption in the Grief Seeds fed to him and on Walpurgis Night gains the ability to force it all upon the strongest puella magi in the immediate area. If a stronger puella magi makes for a stronger super-witch, Kyubey would obviously want to make a contract with Madoka, who would likely have enough power to encroach the entire universe with her barrier.

Also concerning the above theory.
Kyubey is waiting for Walpurgis Night so he can have an all-you-can-eat buffet of Grief Seeds - but the only magical girl who could defeat that many witches alone is Madoka. She's literally his meal ticket.

Being a magical girl is not only a Fate Worse Than Death
But to  since they were once. To make the three previous theories above EVEN worse. The deceased cannot be sent to the afterlife, because their Grief Seeds  are taken away and used by Kyubey as batteries. So they will live in eternity cramped up in a Soul Gem or settling in Kyubey's stomach.

The strongest witch will be encountered in Aokigahara
Where else would be more appropriate? And if not in the anime, perhaps one of the spinoff manga.

Note that it may not be the last witch fought, which I still believe will be the one from Madoka's dream.

Kyubey plans
If Madoka has the potential to be powerful,  like Kyubey says,.
 * Kyuube says he can make Madoka a god, and Homura then says Madoka is self-sacrificing, i.e The Messiah. Magical girls prevent others from suffering, but they suffer themselves. Witches are the opposite of magical girls, causing suffering to others. If Madoka becomes a self-sacrificing god, then
 * Funny how you say that. He made her Christ...

Witches are purging their despair
Collected from the forum thread:

Grief seeds collect darkness from the gems; if they collect enough darkness the witch is reborn; dark gems turn into seeds. As witches kill people, their seeds become more valuable -> by killing people witches purify themselves. Witches kill people by dumping their despair into them - killing them in order to purify itself. If a witch fully cleanses herself, she transforms into something else. QB for some reason does not want this, so he sets magical girls on them - they kill the witches, feed more darkness into their seeds and give them to QB. He later replants them and the witch is reborn.
 * Second-tier WMG: If a cleansed witch transforms back into magical girl, Homura is one such transformed.

The OP is a Spoiler Opening
Let's see. Everyone is looking for minor changes between each episodes' OP to see if it reveals any important plot points. However, the biggest hints the OP has given of things that happened much later so far are in the parts that haven't changed at all. Take the scene with Madoka at her desk, for example. In this scene, she is thinking of all of the reasons why she doesn't want to be a magical girl. Some of these thoughts include:
 * Being surrounded by spiders while thinking about being outside. This could be seen as a representation of the nightmarish properties of the witches' dimension.
 * Being attacked by a Sand Worm. This could be seen as a spoiler for episode 3 and
 * Having her body inflated. This could be seen as a (minor) spoiler for episode 4, where she is subjected to Body Horror
 * Being carried away by crows. This could be seen as a spoiler for episode 6, where it is revealed
 * Crashing into a lamppost while riding a broomstick. While the crashing isn't a spoiler, the very fact she is riding a broomstick in the first place could be seen as a spoiler for episode 8, where it is revealed that The scene which shows Madoka in a Stripperiffic outfit that follows straight after that could be seen as a spoiler for

...and that's even not even take the rest of the OP into account. If this theory is true, then it is highly likely that the theory is also true, considering that she is seen with an older Madoka when making her transformation in the OP, but  is the one that she has to make physical contact with (going off  contract formation sequence) in order to to transform in the anime itself.
 * Actually, putting aside the fact that, the lyrics to both the OP and the ED are surprisingly relevant to the plot especially after watching episode 10. "I won’t forget the promise we made"? The very FIRST line of the OP. "When can I see again here the future that I lost?"!? "destroy one of the dreams of a world racing towards destruction"!? COME ON, PEOPLE, HOW WERE WE SO BLIND ABOUT THIS FACT!? AND THOSE ARE JUST A FEW OF THE MANY RELEVANT LINES IN THERE.

The mysterious Prologue Witch is the result of a Fusion Dance.
The witch's spell circle has multiple symbols on it. The inner most part of the circle, as seen here resembles a pointed flower. The next ring out has a bunch of strange letters. The next ring is the bizarre line of Tomoe. The outermost ring has symbols that resemble a spade in playing cards, or more specifically, something containing the spade.

Essentially, the spell-circle appears to be a combination of symbols, which suggest that the witch is a composite entity; a witch formed from multiple witches.

It seems to be no coincidence that viewers guessed that  based on similarities with her and the Prologue Witch. It would make sense that she would be one of the witches that merge into the Prologue Witch. The other witches? Well if the Came Back Wrong theory is true


 * Also take note that Kyubey is an "Incubator"... And he "takes care" of "used up" grief seeds...
 * Alternatively, on Walpurgis Night, all of the witches not defeated or eaten by Kyubey will combine and try to destroy the world. The resulting creature is the "it" Homura is trying to defeat.
 * As of episode 10 we know that witch is the Walpurgis Night, named after a gathering of witches, adding further credibility to the theory. If so it and its powers may have been changing depending on
 * We can even get a Faust reference out of this, though it would be from a different version of Faust than the one referred to in Madoka. If Walpurgis Night is a Fusion Dance, it can then be thought of a horrifically twisted version of You Are Not Alone (a recurring theme in this series). Well in Marlowe's Doctor Faustus it's none other than Mephistopheles who says "Solamen miseris socios habuisse doloris (It is a comfort to the wretched to have companions in misery)" or more simply "Misery loves company". Being that witches are embodiments of despair, it only makes sense they would bond - literally! - with others like themselves.
 * Supporting this theory is that in Episode 12, when Madoka greets her, she splits into a circle of girls (though this could just be symbolic and they could all be the same girl).
 * Supported by the witch card, though not confirmed.

Walpurgis Night Isn't a Witch.
This is an alternate theory to the fusion dance theory.

In episode 12, we see Walpurgis Night in full view. It appears to be white, like Kyuubey, and its arms look suspiciously like the flaps of skin that come out from Kyuubey's ears. Supporting this theory, Walpurgis Night doesn't have a barrier, nor does it drop any grief seed. And despite being visible to the naked eye and capable of causing the End of the World, no normal human newscaster even noticed a WTF Eldritch Horror in the middle of the hurricane/earthquake.

Everyone refers to Walpurgis Night as the "strongest witch", of course, but this is probably only because Kyuubey said that it was, since the mahou shoujo can't prove otherwise. Of course Kyuubey doesn't lie outright, and this isn't a outright lie either. The Walpurgis Night probably attacks by using the grief seeds that Kyuubey has collected for it, thus making it the master of all witches and thus is the strongest witch From a Certain Point of View, and Kyuubey is infamous for his love of the usage of From a Certain Point of View.

Of course, Walpurgis Night would destroy the earth, which would go against Kyuubey's plans, or would it? As far as a remember Kyuubey only said that would destroy the earth. I can't remember him saying anything about Walpurgis Night itself destroying the earth. Not even once. Yet again, an example of Kyuubey choosing his words in such a manner as to trick the mahou shoujo to do his bidding.

Instead, the purpose of Walpurgis Night's existence is to cause enough death and destruction to make girls into mahou shoujo and

To address the final standing point, its appearance, it is possible that incubators have a system which is similar to how bees and ants work on Earth.

The world where Madoka Magica happens is actually a dream world created by the real Madoka
This is a mix of some theories presented here, and mashed up with some new ones, courtesy of a pic in the Puella Magi wiki, here.

Back in the real world, Puella Magi are not born from contracts with Kyubey, but rather, from a human experiencing a traumatic experience in her life. Witches are still created the usual way, however.

Madoka was a normal person, with a lot of dreams and aspirations, until she witnessed her entire family being brought to suicide by a witch. This event was the trauma that made her turn into a Puella Magi. Like in the series, her magical potential was enormous, practically godlike. With that power, Madoka created Kyubey so that others could help her fight witches if they wanted to do so, and gave power to her pet cat, Homura, to help her in battle.

However, although Madoka was full of determination, her life had suffered a very drastic, dramatic change. Nevertheless, out of a self-sacrificing sense of duty, she kept fighting and trying to make a better world for everyone. It was all in vain, however. No matter how much she tried, people she loved died or fell into despair and turned into witches. Ultimately, Madoka couldn't take it anymore, and her cries of despair ruptured the world as she turned into a witch herself.

After a long, terrible battle, Madoka, the ultimate witch, was subdued, but her friends didn't have the courage to kill her, or it was outright impossible to do so. Instead, they joined forces to seal her and themselves into a dream world where her inner self could live a happy life, free from the pain that being a Puella Magi involved. Kyubey and Homura were tasked with watching over the seal so that Madoka's physical body didn't escape into the real world.

However, Kyubey grew sick of the light-hearted slice of life going on in this world, and longed for the good ol' days in which he was by Madoka's side, killing witches and setting the world on fire, and ultimately decided that this dream world he had been told to watch over was nothing but a cowardly lie spun by Madoka's so-called friends to pull her away from her true life. And so, he tried to get Madoka to awaken and return to the real world.

Homura found out of Kyubey's betrayal and used her powers to reset the time stream of the dream world. This had the effect of everyone forgetting almost everything about their past lives and believing that the dream world was the real world all along. Some residual impulses remained, however... Among them, Kyubey's obsession with getting Madoka to 'awaken', Homu trying to stop Kyubey, and Madoka's depression in general. Should Homura ever fail to stop Kyubey, the ultimate witch will be unleashed on the real world, with catastrophical consequences for humanity.

Unfortunately, dreams are bound to end sooner or later, and so, Kyubey's victory is inevitable. It's not a matter of 'if', but of 'when'.

...or, the whole story takes place in a witch's dimension
and the witch involved is Madoka. If the idea that Witches = Reality Warper holds true then Madoka, being the most powerful witch, should have the ability to create such an intricate alternative dimension where her wishes are kind of fufilled. Not sure why it's starting to break apart though...maybe a magical girl just entered??
 * See also: Pillar System Theory

Madoka will become a
Kyubey sees that Madoka's Magical Powers and Idealism won't make her  too early, the right age to turn into   being adult. Homura is trying to stop her because she's afraid that Madoka will mess up and thus not become  but. That's why Kyubey wants to kill witches even though : they aren't real witches, in a sense.
 * Seemingly subverted in episode 10, where Witch!Madoka brings about The End of the World as We Know It in an alternate timeline.
 * She has a desire to create a perfect world, so whether this is Axe Crazy or not is up to you.

There will be a witch that will maintain its
And odds are it will be
 * Don't count this theory out just yet:  may be based off the Brocken Spectre. The Brocken was a mountain peak where Walpurgis Night (in both Goethe's Faust and German folklore) occurred. The Brocken Spectre is a magnified shadow.
 * Note that those monks in the end look pretty human. They're not the same witches though.

Some (or All) of Urobuchi's trolling is actually him dropping real half-truths of the plot

 * Before episode 3, he claimed "We still haven't shown even a single scene with bloodshed!". Hints at how Kyubey being slashed viciously by Homura (albeit offscreen) in episode 1 doesn't count as blood being shed. Cue episode 8....
 * "Kyu" in "Kyubey" comes from "cute". He wasn't lying. In japanese the 'kyu' from Kyubey shares the same kana as both cute and incubator. The audience has a million to one chance of guessing the correct english word... but still...
 * Kyubey isn't evil. He just has different moral standards.

Homura acts stoic at least in part just to spite Kyubey.
She can never stop being a puella magi, but if Kyubey's ultimate goal is to harvest the energy produced by her emotions, she will feel nothing, damn it. Of course, part of it is just plain desensitization.

The tree-like structure in episode 1 is
The witch is dead, but... Given the impression that the inside structure and color theme  and the implications in the scene that the. If this is true, the dead body of Sayaka will be missing for no reason for the next few episodes. The colored water representation of both girls also implies this happening.

Epic Fail awaits Kyubey.
Sure, he'll save the universe from heat death, but he'll overload the universe with so much energy it'd blow up anyway.

Kyubey lies.
He's not the alien you think he is. Plus he already lied to Kyouko once. Saving the universe from entropy and heat-death is impossible. It's like saying that a Perpetual Motion Machine(wiki it) is possible without a magnet or any net input of energy(it is not). Subtle laws govern physics, much more so with Thermodynamics. There will always be wasted energy until energy is dispersed evenly, throughout the available space...

Alternatively, Kyubey always tells the truth, but there is still a way he can give out false information
He can give out false information if he believes that information to be true. This allows Kyubey to lie about his true purpose; "saving the universe from heat death" is not at all true, but he was created to think that it was.

The reason not even Kyubey knows his real purpose? It's so others can't learn about it as well, until it's too late.

A variation of Mephistopheles will be used as a name for a witch, probably
Because  is too good a pun to pass up. Is it a pun in Japanese too?
 * Mephistopheles doesn't fit the witches' Stellar Name Theme Naming, but Mephistophilia would.

For that matter, there will be a witch named after a Valkyrie
We got a witch named Kriemhild, so why not? Brunhild would also fit the Stellar Name.

Kyubey wants Madoka to make her contract during Walpurgisnacht, no sooner, no later.
First, let's review some key points:
 * A puella magi's power level and abilities depend on the wish she made.
 * As proved by episode 8, the characters are, to some vestigial degree, aware of the alternate timelines.

Given these two points, Kyubey knows what he needs to do: contract Madoka on Walpurgisnacht. Episode 10 demonstrates that whatever wishes she made at other times didn't make her powerful enough to be able to change the laws of nature. That one time she turns into a thundercloud-witch implies that she's likely still very strong, but not as strong as Kyubey keeps telling her she would be in the current timeline. Whatever wish Madoka made on Walpurgisnacht in the previous loop did make her powerful enough, however—and Kyubey can remember it happening. So this timeline, he'll try to do it again. We can only wait to see if he's successful or not...

It's never really been about Madoka.
Episode 10 reveals that

From this, it seems rather likely that  shenanigans with Madoka are simply one big Batman Gambit to keep   real target, Homura, occupied until. So long as she doesn't think about things too hard until that happens, she won't realise she's being played like a Stradivarius. Indeed, it's likely that
 * It should be mentioned that . However when he figures it out, he goes along with it for this reason.

Sayaka never had a chance with Kamijou
During the third iteration none of the girls really believed any of the crazy things about Soul Gems that Homura told them. So Sayaka presumably had no reason to avoid confessing to Kamijou. Yet she still becomes a witch. Moreover, a witch that really hates Hitomi. Obvious conclusion: Kamijou just isn't interested in her that way, but he does like Hitomi. Which would also explain why the current Kamijou has been completely ignoring her.

Walpurgis Night is a different witch (or collection of witches) each iteration
This seems obvious. They all bear resemblances to each other, but they're never exactly the same.

Of course, this Walpurgis will be the worst of them all.

The reason there are five timelines is because Four Is Death
Confused? Think of it in this way: Homura has gone back to the past four times. Of course, you could argue whether Four Is Death applies to the loop or to Homura...

Mami and Kyoko became witches in previous iterations.

 * For Kyoko, it could have been in iterations 1, 2, or 4.
 * For Mami, it could have been in iteration 4. It's also possible it could have occurred in iteration 2.

Homerun has traveled to the past more than 4 times
We seem to assume what we have seen is all that has happened. However, it could be more of a case like in Higurashi no Naku Koro ni. Or it could not be like it since Homuhomu has tried to change fate herself from the start unlike in the mentioned example. Although we have yet to see if there is any indication about she doing it many more times than we have been shown.
 * Her character development in the first three iterations wouldn't make sense if there's more, the 3rd leads directly to the fourth, and the fourth ends with the prologue. There's no room for any more
 * What I had in mind was that some timelines could repeat and be very similar. So the room for more would be any timeline after the fourth. But since she is not the kind to sit and wait for something to change, even I thought it is more likely that there have been no more timelines than the opposite.
 * In episode 11, QB says she has looped 'countless' times. He can probably count past five. When asked how many girls she's seen die, Homura herself says 'too many to count.' Any other timelines would likely fall between the fourth and fifth.

The cause of the Walpurgis Night
The Witch of the Walpurgis Night is actually a way to balance out the Puella Magi - Witches quantity. If there were too many Puella Magi in an area, the number of Witches would diminish faster, and the. So as a counter-measure, by some kind of method, the Walpurgis Night Witch is born.

For example (just a possibility), maybe when a Witch dies, its residues reunite with other Witches' residues in some secluded area and start forming a special Grief Seed which cannot be detected by the Puella Magi due to its low activity level, until this "egg" is strong enough to hatch and give birth to the Walpurgis Night Witch.

This Witch would not only create a huge amound of energy itself, it would also hugely reduce the number of Puella Magi (and ), so that more witches can reproduce. Slowly, more girls would be contracted to fight the newborn Witches, repeating the cycle.

Yes, you should have noticed what I've implied there: The Walpurgis Night has happened many times before. The devastating effects caused by this Witch are probably explained in the real world by a)Natural disasters or b)Human causes (huge wars, genocide, etc.), AGAIN, as a WMG above mentioned.
 * It showed up at the same time when there were only two magical girls around and when there were five, though
 * Yes, I noticed. But my point here was that there is some kind of "time limit" for the girls. If you don't die before this night, you will die during it anyway. The Witch wouldn't differentiate about how many there are left, it just appears at a certain time to do its ass-kicking job.

The title character of the soon-to-be-released Prequel manga, Puella Magi Oriko Magica, will become
Because the piece of promotional artwork marks her as a Token Mini-Moe, and she's seen with Mami and Kyoko.
 * Another thing. Homura is mentioned to be appearing in the series. Since it seems unlikely that Oriko will take place in the week between, it's possible that we will see Homura  . A likely reason we would see her there is because
 * Homura boldly kept Charlotte's grief seed, partially so Kyuubey wouldn't dispose of it and it could be useful (and keep it away from Sayaka and Madoka), and partially because she might have recognized Charlotte.
 * We may actually have a piece of evidence for this: Remember the runes in Episode 3? The one that basically went " Mami"? The line before that one is apparently the origin of Homura's Fan Nickname Homuhomu. Now remember the following:
 * Should be mentioned that if Oriko does call Homura  it would still fit with her "people don't usually call me by my first name" statement in episode 10.
 * Preview pages of Oriko Magica show that the girl on the cover IS NOT Oriko. However, she can still be the Mysterious Green-Haired Girl.
 * Jossed

Elsa Maria was
Kept here for archival purposes, as it was a common fan theory when Episode 7 came out. Should be noted that it's very unlikely: This theory would require an implausible set of Contrived Coincidences...unless the (equally unlikely) Came Back Wrong theory is true, in which case all bets are off.
 * Regardless of this theory's validity, there is nothing that says . This might then be something that comes up in Oriko.
 * At this point, the only way this theory is possible is if her wish was something like " ".
 * Not necessarily.

Kyubey is using Homura as his Unwitting Pawn.
Stop to think about it for a moment, reflex. We find the key of this theory in episode 10. .
 * A point: if Kyubey is to be believed, 'surpassing entropy' is the whole point of making Peulla Magi and witches. Every time a prospective Peulla Magi makes a wish, they surpass entropy.

From this, what can we deduce? That Kyubey is laughing his ass at Homura and her puny attempts to save Madoka. Everything that has happened in the series was all part of a plan that was set in motion. From this point on, there are a few possible outcomes:
 * Homura manages to defeat Walpurgis by herself. . Kyubey wins.
 * Homura doesn't manage to defeat Walpurgis by herself and dies, and Madoka makes a contract with Kyubey. . Kyubey wins.
 * Homura doesn't manage to defeat Walpurgis and dies, and Madoka does not make a contract with him. Kyubey still has a consolation prize . Kyubey wins.
 * Homura finds out that she has been being manipulated from the beginning, but finds no way to foil the plan. Homura dies . Madoka makes a contract to try and save Homura. Kyubey wins.
 * Homura somehow finds out that she's being manipulated and finds a way to foil the plan. Kyubey loses. But finding out this would require of plot omniscience capabilities that Homura, simply put, doesn't have, or alternatively, a lot of luck. Therefore, this is very unlikely to occur. And even if she finds out of the manipulation, there are no guarantees that she can foil it in some way. And even if the plan is foiled, Kyubey could simply go look for suckers to farm elsewhere. The plan continues as intended. Kyubey wins.
 * Kyubey wins.
 * Conclusion: This is all one epic Xanatos Gambit, fated to bring a satisfactory result to Kyubey, and Homura has no way to stop it. Game Over. Kyubey WINS.
 * What would happen if
 * That's pretty much the incubator plan, yeah. Even if they run out of witches and Puella Magi, well, in that case they can still find girls who are willing to make a wish. After all, a Puella Magi who can't purify their soul will transform into a witch... and the incubators get a benefit out of creating Puella Magi, and allowing witches to form. Preventing the witches from destroying humanity is in their interests, too, because no humanity means no more Puella Magi wishing and no more witches cursing.

The witch Roberta, from episode 10, was
Taken from the Puella Magi wiki.
 * Unlikely since Roberta seems more like a Bottle Fairy.

Homura still has a part of her that is a shrinking violet
Probably justified due to the fact that she has a number of Not So Stoic moments and her ever present lack of social skills.
 * Seen in episode 11, though I don't know if you can call that shrinking violet.

The effects of a Puella Magi's wish have No Ontological Inertia
Especially if it's a Selfless Wish, so for example,

Cross-posted Ending List from Puella Magi wiki
Pretty much every possible ending there is, right here. Ratings are:
 * Happy Madoka and Homura: Happy Ending.
 * Sad Madoka: Bittersweet Ending.
 * Madoka Crying: Downer Ending.
 * Madoka in pain: Kill'Em All
 * Kyubey-eyed Mami: Gainax Ending.
 * Kyubey: Troll Ending
 * Bittersweet Ending achieved.

Kriemhild Gretchen is
Kriemhild means  Coincidence? I THINK NOT.

The title character of the spin-off Kazumi Magica manga is actually a
Kazumi has signs of a Dark and Troubled Past, even referring to her amnesiac self as a "new Kazumi" as opposed to the "old Kazumi". At the end of chapter 2, her friends say that  And let's face it,

Of course, the anime has said that such a thing is impossible, which is why this WMG must be taken together with the next WMG
 * Although this is unconfirmed, we can say the amnesia and outfit have nothing to do with this.

Kazumi takes place after the anime, specifically after
Specifically, a  Part of the changes would include a way to. Note that the black cat in Kazumi chapter 2 resembles the one seen in the OP of Madoka (and in a piece of official artwork with Homura). Earlier guesses on this page say the cat could be
 * Extremely likely given Madoka's wish. The only contradictory part is that in Chapter 3 we see a Grief Seed much like the ones in the anime, not the cube-like shapes Homura has in the end.
 * Nearly Jossed as of Chapter 4.
 * Jossed six ways to Sunday in Chapter 5.

Kyubey's species...
...is actually comprised of humans, or reincarnated/converted/modified humans.


 * Oh god, the Incubators

It is possible to get a human back from being a witch, Kyubey just didn't know and Kyouko made the wrong choice.
Sayaka wouldn't listen to Madoka even when she was a human. What Kyouko should have done was gotten Hitomi to come and apologize or try to smooth things over.

Hitomi already is a magical girl.
She visited Kyosuke at the hospital like Sayaka, and asked him to keep it a secret not only because she was aware of Sayaka's crush on him, but she was unable to face up to her own feelings. Kyuubey asked her to contract roughly halfway through the show, and she was going to wish for the courage to confess when Kyosuke was suddenly discharged. Either by asking Kyuubey or figuring things out on her own, she realized Sayaka was also a Puella Magi and gave her the first chance at confessing for making a more 'selfless' wish; she also didn't want to pull Kyosuke away from someone who could be his true love. When the deadline passed, she made her wish, but never got a chance to reveal things to Sayaka (who she didn't want to make an enemy of) or Madoka (that may have been why she told her to wait at the start of episode 9, however). She's been avoiding other Puella Magi, hiding her Soul Gem in her school bag, and not sending telepathic messages to keep the secret. She doesn't know the specifics about witches just yet...
 * Oh, and her power is punching people in the stomach.

Walpurgis has teleportation or time-travelling powers
...but I don't know how to explain how. Maybe
 * Now, first off, in the episode where Homura is discussing Walpurgis with Kyoko, Kyoko doesn't seem to know when, where, or even if Walpurgis will appear in the city. This leads to...
 * Point 2. We don't ever hear anything about any city-leveling earthquakes (ahem) happening progressively closer to Mitakihara, which makes me think that...
 * Walpurgis will just appear out of nowhere over the city. And the two powers that I know that allow for that are teleportation and time-travel.
 * If it is time-travel, this would make the  WMG even more likely.

Witches can be revived by other witches.
Kyuubey says that a witch can be revived if a magical girl uses its Grief Seed too many times to recharge magic. The process of recharging magic involves putting the darkness from inside the Soul Gem into the Grief Seed. It's only logical to assume witches can do something similar with their own Grief Seeds, especially since

As a corollary, this is the reason why Kyuubey devours "used up" Grief Seeds. If a roving witch stumbles across a nearly-revived Grief Seed, it could easily get a new ally. Two (or more) witches working together might be enough to quickly defeat a magical girl, and Kyuubey has some interest in keeping magical girls alive

If this theory is true, there's a bit of Fridge Horror: Who here thinks that Homura gives her Grief Seeds to Kyuubey? Anyone? It's highly doubtful she does so. Meaning she probably keeps a stockpile of Grief Seeds somewhere. They're probably kept in her Hammerspace shield, but it's also possible they can be removed somehow. And if she keeps her seeds somewhere else? We only need a witch to stumble across it, and then...Why hello, Charlotte!

Kyoko knew magical girls could become witches, but not that soul gems were their souls encased as gems.
She seemed very worried about Sayaka's gem darkening, even though Kyubey apparently never told what would happen if the gem became completely dark. Perhaps she've seen a fellow magical girl become a witch before Sayaka (Elsa Maria, perhaps) and thought that becoming a witch corrupted her soul gem, killing her in the process, but never really knew that Puella Magi, as well as herself, were Soul Gems.

Walpurgis Night is powerful because it's a witch that can fuse/reunite with other witches.
The witch we see is just the result of the fusion. The girl who became a witch probably wished to not be lonely, or to have many friends, thus, enabling her, as a witch, to fuse with other witches and become really powerful.
 * Implied by the witch card but not directly confirmed.

Kyubey recycles Grief Seeds on occasion.
It has shown that a defeated witch's grief seed has a usage limit, or else, the witch might wake up again. Perhaps Kyubey has a way to recycle it into the same witches, over and over, by putting said Grief Seed near places where people tend to have negative emotions (like schools, hospitals and places where people tend to commit suicides/crimes; Charlotte's Grief Seed could be a recycled one). It could be a way to not extinguish the planet's power source so quickly, as well as a way to invite new mahou shoujo and make them able to defeat witches for a while before becoming witches by themselves. The way he "ate" the Grief Seed was different from the way he ate his own corpse; actually, he could be storing the Grief Seeds for later reuse, instead of just plainly eating them.

Walpurgis Night's motivation will be to Put Them All Out of My Misery
Derived from Homura's Nietzsche Wannabe speech in Timeline 3. The idea is that Homura's "turn this world upside-down" comment does refer to Walpurgis, but it doesn't mean Homura will become Walpurgis. Rather her line acts as Foreshadowing for Walpurgis's goal - destroying everything to end suffering, out of its own suffering. In this context, the line "become monsters together", can be thought to support the "Walpurgis is a Fusion Dance" theory.

For maximum effect, there will probably be a Meaningful Echo. "Destroy, destroy, destroy it all!"

Walpurgis Night will be "born" from that giant tree that keeps appearing
Every time Walpurgis is seen, a giant dead tree is somehow also present in the city. Since witches have Grief Seeds, it only makes sense that one of the most powerful of witches would grow from a giant tree.

The incorrectness of Kyubey’s energy/entropy theory was intentional.
The use of energy – energy cannot be created or destroyed (first law of thermodynamics). It does however get turned into heat (second law of thermodynamics), so eventually all usable energy will become heat, and no energy input will result until some kind of energy output (from the heat) happens.

What Kyubey is doing is saving the universe from this, not loss of energy altogether. Thus with all the witchery and magic Kyubey is creating usable energy, i.e. adding to the total amount of energy to the universe. This leads to usable energy plus the energy converted to heat.

The result? Said created usable energy will also be converted to heat, as he gains more usable energy that will also eventually become heat. The mass accumulation of energy that eventually becomes heat gathers together and eventually there will be enough heat to burn up the universe and everything in it, or at least make it an unlivable place to be in.

Thus, Kyubey’s part of a mass effort to destroy the universe. Whether this is intentional or not...
 * That's. . .what Kyubey was talking about when he was referring to the heat death of the univers- in episode 10 he actually refers to it by name, as entropy.

In one of the alternate timelines, Sayaka was in love with Hitomi.
In the current timeline, when she became Oktavia von Secekendorff, her barrier resembled a concert hall with violin-playing familiars, including one who looked like Kyosuke. However, in the alternate timeline, she had a rock stage and dancing familiars that resembled Hitomi, not to mention that alternate!Oktavia's card mentions her favorite sound being a guitar, not a violin. Clearly, they fell in love or broke up at a rock concert and Sayaka went mad with despair.

Kyubey uses Grief Seeds to fuel Walpurgis Night.
Because the whole Magical Girl process is already a Vicious Cycle, there's no reason why the cycle shouldn't end at Kyubey just making the things disappear. Besides, it seems as though WPN is a regular occurrence, or a least one that can be predicted.
 * Alternatively, Walpurgis Night occurs naturally, but Kyuubey is going to use his stored Grief Seeds to increase this particular Walpurgis Night's power, in order to force Madoka into becoming an even stronger magical girl

Walpurgis Night does drop a Grief Seed (or multiple Grief Seeds)
It's just that when it dies, the Grief Seed(s) scatter across so wide a area that they're hard to find. It/They may even fly into another town, and the Vicious Cycle repeats again...(especially if the Incubators can revive witches from Grief Seeds).

Charlote .
The idea came from this fic. Might also count as Fridge Brilliance.
 * So, it wasn't obvious from the start? Not to mention that Mami had, well, big milk producers.

Nothing is real (a.k.a. the Homu-space theory).
Everything is in Homuhomu's head, henceforth known as "Homu-space". The entire series is a dream sequence while she's in the hospital, and the restarts are akin to the classic dream-within-a-dream scenario. This would explain why all these fantastic things are happening around her, but her power equates to a glorified pause button and a Hammerspace shield. She escapes from Homu-space when she finally saves Madoka, or for absolutely no reason in episode 12/13 for trolling purposes.
 * Bonus points if we're lead to believe this is the case only to have it averted at the last minute, or when she does wake up for real, that she lives in a "regular" world like ours (i.e. not quite as futuristic).
 * Double bonus trollpoints if she wakes up, realizes everything was a fabrication and Puella Magi/Madoka wasn't real, and then hangs herself.

Kyubey is trying to create a pepertuum mobile
That's why he granted Homura her powers. His goal is to create something that will eternally consume unusable energy and transform it into usable energy, thus defying entropy without having to destroy more magical girls. That's also why he's called Incubator.

Homura
Knowing Kyuubey, he likely decided to in a way that wouldn't make her a threat, but would allow him to meet his energy quota. To make this even worse, I'll tie it in with the theories that

There's one wish Kyubey can't attend.
Said wish is exactly the one to reverse entropy (thus, preventing the heat death of the Universe). If Kyubey made it real, things would be simpler in the start, but, the witch that would come out of it would destroy the whole Universe via instant heat death, rendering the whole deal completely pointless.
 * Then there was the Gainax Ending in Episode 12, in which  so this wish is entirely possible to happen.

Madoka's Wish is to be useful.
She's always moping about not being useful and just wanting to help people.
 * Jossed for this timeline, unsure about the previous.

"Puella Magi" is not synonymous with "magical girl".
We've assumed it's what Puella Magi is due to how it was fit in the title, but in fact it means something else.

Perhaps, related to the "Madoka will become a True Magical Girl" theory, "Puella Magi", or "girl of the mage", is Madoka's True Magical Girl name. (Just one suggestion.) This will have the side effect of forcing all of the wiki writers and fansubbers to change all of the instances.

Keeping in mind Episode 12, it may be the name of Madoka's Goddess Form.

Madoka didn't
still has his quota, and the creation of a witch is still the best source of energy around. She ended his current means of going about it, but nobody ever said anything about him not finding non Puella Magi contract-based ways of  afterwards.
 * Hell, depending on how narrow the wish was interpreted, he may simply move on to Puer Magi.
 * Keep in mind that her wish was retroactive. If that was the case, the Incubators would have to move pretty slowly not to have figured it out within the last 5000 or so years.
 * He gets it from Demons now. Anyone can become a Demon Slave (Word of God says they suck humans in and enslave them) (called "Witches" in Puella Magi Kazumi Magica) when they get too much Despair; except for Magical Girls; who die when they reach the Despair Threshold.
 * Until there's a girl who wishes that they could erase demons before they became such. Then, there'll be Madoka to erase the witches, the other girl to erase the demons. And Kyubey will have to, somehow, work his way around it.
 * Keep in mind though that Demon Slaves can return to their human forms, unlike witches (e.g. Kazumi chapter 2). So the universe is definitely a lot better.
 * Kazumi Magica is actually very likely to take place before or during the anime, where are you getting this stuff from?

Related to above, Gainax Ending Sequel Hook suggests that
...which will be the new enemy in Season 2. Also, did anybody notice that there was only with Homura?!
 * Found support for this (obviously has spoilers): This cut of the ending has a relation to Hecate, who is a witch, and The Hydra, which has multiple heads, both Greek mythology. Combine the two together, and you have the picture of heavy Symbolism.

Madoka wasn't the first to make a Reality Warper-level wish
In episode 9 Kyubey states that there are some things about magical girls that even his creators can't explain. Then, in episode 12, he states that he has no idea why Soul Gems disappear when they're used up. My theory is that at first magical girl powers were completely explainable, and somehow the rules were even worse than they are now. But then a powerful magical girl made a wish to change the rules and managed to move the Sliding Scale Of Idealism And Cynicism just slightly more towards idealism. She, like Madoka, Ascended to A Higher Plane of Existence, resulting in Kyubey forgetting both her and the wish. This could have happened multiple times, with each girl adding a new wrinkle to the rules that Kyubey can't explain.
 * Perhaps, at the end of the universe, someone wished for a way to reverse entropy, kicking off the biggest Vicious Cycle of all time.
 * "Even worse than they are"? Not particularly difficult. What if the Incubators' power had originally been in the hands of humans?

A Puella Magi's desires extend to even what her outfit looks like.
How else was Madoka able to somehow perfectly predict what her outfit would be?

Madoka wanted to be one of those fulfilling heroine-magical-girls, so she drew herself that way in her notebook and thus came out looking exactly like that. Homura wanted to be the bold, brave protector, and thus her outfit has many straight lines and sharp angles, giving a sense of don't-mess-with-me. Kyouko wanted people to listen to her father, and her outfit gives the feel of an aristocratic messenger. Mami's can't be defined since nobody knows what her desires besides
 * Madoka

Hypothetical Season Two predictions
If the previous season was Part 1 of Goethe's Faust this will be Part 2, which is more episodic in nature. The episodes can be a bunch of vignettes dealing with the lives of the characters  If we're lucky, we may even be treated to   The main plot will probably focus on   If the Faust parallels continue, the end of Season 2 will be   If we're really lucky they may throw us readers a bone and , but don't hold your breath.
 * Urobuchi said a potential Season 2 would probably be just a Slice of Life story without any real plot, but then again he's also a lying liar who lies.
 * Actually it was Shinbo who said that. Still, a Madoka-less Madoka Magica seems likely, unless the scene with all the magical girls was Foreshadowing.
 * Although, by that time, we would be following the real driver of the storyline.

The Stinger speculah
1) Homura is in an apocalyptic world, in the far future or even in the near future. Madoka is egging her on, but Homura is about to die; she hears Madoka because of this, and her ties to fate show.

2) Homura is inside a demon's barrier and Madoka still has a connection to her.
 * This scene is depicted as taking place in a Black Rock Shooter/Tartarus-like dungeon with checkerboard floors in the manga.

3) Mami and Kyouko may or may not be dead.

4) Some mixture thereof of the facts of the last three points.

Homura's wings in The Stinger
Are a manifestation of her witch form.

But instead of becoming a witch, she'll manifest it as a Guardian Entity. Oh yeah, we're getting Stands.
 * This also relates to the above WMG (Gainax Ending Sequel Hook). See that for more information.

Tatsuya can actually see Madoka.
Considering he treats her like an actual imaginary friend, maybe he can even see and interact with her (though not in a physical level the world can see).

Madoka killing Kreimhild...
...was a Battle in the Center of the Mind.

Kyubey was right.
The series up to the end of Episode 12 was all in Homura's head. Madoka never existed. The "happy" system had always been the system.

Anne Frank's wish was to be a famous author.
Unfortunately for her, it didn't happen until after her death.
 * It is true that she planned for her diary to be published in the hopes she could become famous. (She also had dreams to go to Hollywood, I think, though I think it's unrelated.) Perhaps her fighting witches was what caused her to get caught...
 * The world war 2 must have an end, so it's natural planning to have the diary published if she or her family have any chance of surviving it.

Dark Angel Homura is the result of a mental paradox; as well as driven by her oath.
Homura will protect the world; so she won't let herself get killed by the Demon Beasts. She knows that if she absorbs too much darkness than even Kyuubey can absorb; she will theoretically succumb to the despair and see Madoka again. Which gives her more hope than anyone. She knows that Madoka would never let her fall to darkness, and her hope at seeing Madoka again when she does gives her a capacity to absorb more despair than any magical girl ever.

Kyuubey has a different name in the new world.
Since he's not an "Incubator" anymore.

Pre-witch Walpurgis made a wish similar to Madoka's, but screwed it up.
She wished to save other Puella Magi from their violent deaths, not knowing at the time that they eventually turned into witches. As a Puella Magi's body dies when she becomes a witch, Walpurgis is endlessly forced to roam the Earth, collecting the 'remnants' of their souls to be her familiars (which is also why any Puella Magi fighting her has their Soul Gem corrupt incredibly quickly). Her moment of despair was learning the truth of the system, which reduced her to Laughing Mad.

Charlotte had diabetes.
When Charlotte was healthy, her two favorite foods were sweets and cheese. When she developed diabetes, she could still eat cheese, but not sweet things, so she wished her diabetes away so that she could eat desserts again. The association between her wish and sweets is why, as a witch, her barrier is dessert themed; that same association is also responsible for witch!Charlotte's ability to create sweets. Ironically, because Charlotte's wish had nothing to do with cheese, witch!Charlotte is unable to create any sort of cheese, explaining the description regarding her fixation for it in her witch card.

The following theory is true
Taken off the PiratePad speculah pad.

"I actually thought Homura's black wings in the end were actually "Madoka." Since Madoka is formless now, and only a concept in theory, so they depicted her as a pair of wings surrounding Homura, protecting and embracing her, as if saying that she has her back and is supporting her. This also explains the "ganbatte" Homura hears from Madoka. The ending scene shows their reunion which Madoka promised and reinforces the scene of English text shown right after the ending song: That as long as you remember her, you are never alone. And I don't think the wings look evil. It's black with sparkles (kind of like pictures of space and galaxies), like their bodies when Madoka and Homura hugged and parted in space. It has flowers, like the rose on Madoka's bow, and if you look closely, there are depictions of wheels (both spinning wheels and tire wheels), which are symbolic of time (i.e. Madoka is time itself, existing at all points in time)."

The Slice of Life second season will take place in a Mundane Afterlife.
Specifically in a world Madoka created for the Puella Magi who disappeared.

There will be a super fusion demon named Samhain in the new world.
For those who don't get the Meaningful Name, Samhain also refers to a festival, but this time taking place during October.

Joan of Arc becoming a Puella Magi resulted in Gilles de Rais becoming a child killer
Learning of the source of Jeanne's powers, Gilles went mad like Kyoko's father, believing himself to be slaying demons or at least be "saving" them from the fate of being a Puella Magi.

It seems like a depressing enough scenario to be possible, and in a show like this it seems unlikely that it would mention Jeanne d'Arc and not Gilles de Rais.

Homura worsened the problem that is Walpurgisnacht in the same way she increased Madoka's potential.
Think of it this way. Walpurgis was a somewhat above-average witch that got lucky and managed to kill Mami, thus making her undefeatable due to it requiring a two-person teamwork to beat (or something). Madoka made her Last Stand, while Homura made her wish. On the second iteration, Homura gets stronger, Madoka too, but still they can't beat Walpurgis. It's because Walpurgis, as the other 'Central Core' element in the generated multiverse, also got stronger. It's only logical that for all the potential Madoka gets in every iteration, something has to counteract it. However, this Troper suspect that Madoka's potential gain outstrips Walpurgisnacht's power gain by a rather fair margin (perhaps due to said Last Stand), or otherwise Madoka's final solution won't work after only six iterations (barring any iteration not shown).
 * Also, Madoka's Wish gave her power to "erase every witch." In addition, by erasing her physical existence from the equation, this also had to balance out on the other end as well; making Walpurgis vulnerable.

Kyubey benefits more from the new system than the old one.
Yes, sucking off a lot of power from a Super-Witch is faster; but merely exceeds Kyubey's "quota." It's still finite; especially since Kriemhild would destroy the Earth almost immediately; killing the golden goose that is the human species. A continuous Magical Girl/Demon war provides QB with a renewable resource, that should, if maintained long enough, exceed the power output that the creation of a single devastating witch would harvest.
 * Given how long-term the heat death of the Universe would be (context, in about 100 Trillion years, star formation will end), if QB's race thinks long-term at all; they should know this. You do not slaughter the entire herd of cattle without leaving breeding stock.
 * Addendum: QB did know this, and encouraged Madoka and Homura to make the decisions they did in order to create a renewable system.
 * ...Are you saying he planned it all? Damn...

Kyubey planned everything; including Goddess!Madoka, because he can read minds and wanted a better system.
An elaboration of the above; Kyubey was not "beaten" in the end. He got exactly what he wanted; a better self-maintaining perpetual human being energy factory from Earth. "Less efficient" doesn't mean "destroys itself after one big output." Kyubey can likely read minds; and he's good enough at manipulating emotions (even though he doesn't have any) that a lot of his wonderings about human beings emotions don't make sense (just because you don't feel emotions doesn't mean you can't predict them) unless he's specifically goading them into doing something he wants. He's even tells Madoka she can be a Goddess and tells her everything about the system. He psychically shows her the suffering of magical girls/witches throughout the ages. He wanted her to change the system.
 * How does he keep track of the timelines? He reads Homura's mind and realizes the changes each time.
 * His wide eyes at Madoka's Wish isn't an Oh Crap moment. He's excited he's getting his goal achieved.
 * His "lol witches would be awesome" in the new timeline are to let Homura continue to think he's a defanged monster; instead of someone who got what he wanted; thus he can farm despair from the demons through her.
 * Just as planned...

Kyubey won, Grimdark edition.
Madoka's wish eliminated all witches from the universe - by shunting them outside the universe. This benefits Kyubey because now the Incubators can get the same return (while they may not have figured it out by the modern era, they will eventually) and the magical girls don't even realise it and so won't interfere.
 * Except we see Goddess Madoka purifying the Magical Girls who are about to witchify, and she's smiling. This would require Kyubey being able to manipulate her wish into even fooling her, and nothing implies that level of control over the wishes.
 * Oh, that bit's fine. The issue is what happens after Homura/Madoka's conversation. Besides, we know that witches can do some pretty screwed up things while thinking they're helping people. Remember Kriemhild Gretchen?

Puella Magi are always recreating the universe.

 * It's an endless cycle. The world prior to Madoka's reboot was actually created by another Puella Magi who made a similar wish to change an even worse universe into a slightly better one. Ditto for the one before it as well. This is actually a part of the Incubator's race plan: since they can only temporarely stop the heat death using powers they don't even completely understand, they are harvesting Puella Magi until one of them get's strong enough under the current system and decides to change it, in the hopes that under the newer system, one new Puella Magi might be able to just pull off a "Stop the Heat Death" wish and write a "perfect" universe. However, even they do not know about this plan, either because it's been lost in the many reboots, because it's the master plan of someone higher up, or simply because they don't know it... but hey, unexpected side effect.
 * All the non-grimdark Magical Girl universes come from this, actually.
 * So in the future some other magical girl will become a Groundhog Peggy Sue in order to stop her friend from dying or vanishing. This will cause her friend to become as powerful as Madoka was, and her eventual reality-altering wish will be to create a way for vanished magical girls to come back. Presto-chango: We have a Belated Happy Ending as Madoka and Sayaka come back in the rewritten world.

Witches used to absorb all ambient negative emotional energy before it could coalesce into demons.
In the old timelines, demons could have existed but never had a chance to form. In the witch-free reality, they happen naturally.

When magical girls disappear in the new world, they are taken by Madoka to a Magical Girl Valhalla.
The ultimate reward for fighting the demons, happiness in an afterlife.
 * Director Shinbo stated that he believed this in an interview.

Charlotte wished for cake.
Like Madoka, all Charlotte wanted was to be a Magical Girl, so she wished for cake (making Mami's advice to Madoka an Ironic Echo). But when she realised exactly what she'd gotten herself into, she decided she hated cake, and started eating cheese instead of desserts. That would explain why she can create cake out of nothing (she did just that when she made her contract), but she can't create cheese.
 * The cake is a lie!

Girl!Charlotte had a tapeworm.
But she didn't realize it, so therefore even as a Puella Magi, it was still there. Witch!Charlotte's first form was a cute little doll-thing, and the second form, a worm-like creature, came out of her mouth. Tapeworm.
 * Cancer. It's semi-confirmed by the medicine bottles and the "Operating" sign in the dreamworld.

Homura's heart was cured as part of her wish.
I still found the Common Knowledge about she cured her heart using restorative magic unfeasible, as there's no "normal" state that she could restore to. And then I recall the main point of her wish was (parapharsed) "to protect, and not to be protected, by Madoka." While her visual problems should not be an obstacle to that wish, but if her heart condition forced her to be hospitalized up to the age of 14, it would be an obstacle. So, as a part of granting that wish, Kyubey not only gave her time manipulation abilities, but also cured her heart. Disclaimer: this troper has no first-hand experience on this work, so he may have misquoted.

A Walpurgisnacht Witch consists of deceased Puellae Magi, at least in the manga.
When Kyouko suicide attacks Oktavia von Seckendorff in the manga, we are shown a scene with Kyouko and Sayaka in some kind of afterlife, indicating that some semblance of an afterlife for Puellae Magi already existed before Madoka's Cosmic Retcon. This is Jossed, however, during Homura's battle with Walpurgisnacht later in the manga. Remember how Walpurgisnacht's Familiars resembled Puellae Magi? Well, in the manga three of them are clearly Sayaka, Kyouko and Mami, all of which died in different ways, suggesting that all dead Puellae Magi become Walpurgisnacht's Familiars.

Tl; dr: Walpurgisnight is a recurring event, and therefore more of a force of nature than a simple Witch. If all Walpurgisnachts are the Witch form of the same Puella Magi, it could be that Walpurgisnacht cannot be defeated, and simply comes out periodically to "feed". It is the fate of all Puellae Magi who die, no matter how, between two Walpurgisnights to become part of Walpurgisacht, while their souls go to Puella Magi Purgatory. Only if/when Walpurgisnacht is defeated, would the souls of the Puella Magi be free to travel on to whatever afterlife existed before Madoka reset the universe.

Charlotte was bulimic.
She may have wished for better self-image/self-confidence, only to fall back into her old habits in a misguided attempt to gain control of her life when being a Magical Girl proved too much for her. Her first Witch form is a mouse not just because of the cheese theme, but because she was a Shrinking Violet, and she's a poor fighter because she let bullies push her around and make her feel bad about herself (which would add some real Fridge Horror to Mami's apparent curb-stomping of her). And remember how she unleashes her One-Winged Angel form? She throws it up.

The "second love letter" Hitomi is mentioned to have gotten in the first episode was from Kyosuke...
...which lead Hitomi to develop feelings for him. He couldn't confess his feelings to her at first because he was in the hospital. Hitomi might have realized it was him and started to like him. Sayaka was doomed from the beginning.
 * Either that, or Kyubey wrote the letters knowing Hitomi would fall in love with Sayaka's love interest, which would lead to Sayaka's becoming a witch and killing Kyoko after he doesn't return the feelings?

Anne Frank is in a And I Must Scream scenario.
She was seen holding her Soul Gem on the train ride to Bergen-Belsen. Something like that looks valuable so the Nazis would have snapped that up if they knew about it. So Anne kept it hidden, until one day she's caught holding it and it's taken away from her. Soul Gems being what they are, she would have dropped dead as soon as it was far enough away, and the Nazis brushed her off as another typhus victim. The Soul Gem would have likely been bartered, sold, or hoarded. So somewhere, there is a Soul Gem sitting on a shelf, and Anne stuck inside it. (Heck, that might be a way she became a witch in the pre-Madoka world.)
 * Perhaps she knew about the circumstances when it got too full of despair and hoped it would taken elsewhere for the sake of her family? But if she had the power, why didn't she just break out?

Mami's wish was to live and be able to cook again
So we know that Mami is a mentor, Cool Big Sis, somewhat of a Team Mom to Madoka and Sayaka (and Homura in the other timelines). And you might remember the scene where she takes Sayaka and Madoka to her apartment for the first time and they're marveling over how delicious her cake is. What we don't know however, is exactly what she wished for to become a Puella Magi. Now here's where my WMG comes in - what if Mami had somewhat of a hobby of cooking or baking and wanted to do it as a career? It wouldn't be too surprising considering her mature demeanor and motherly personality. So what if her wish on that day of the car crash was something close to "I wish I could live and make delicious food!" (The last bit could possibly be to ensure that she would have a promising future had fate only been kinder). And adding the whole "balance of hope and despair" thing to this wish, well...just think about how easy it is to turn around the phrase "make delicious food"...
 * Perhaps this is also related to ?

Mami, like Kyoko, is Christian
Not much in the way of evidence, but this rendition of Mami's theme shows just how easy it is to replace the fake language lyrics of the original into holy lyrics of Latin. The Latin roughly translates as "Holy, holy, holy, Lord God of hosts. Heavens and the earth are full of glory. Of your glory". Adding more to this argument is the fact that there is already a confirmed Christian in the cast (Kyoko) and one witch highly suspected of being one (Elsa Maria).
 * Perhaps they're all virtually Christians?
 * The Mitakihara Junior High uniform looks very much like a Catholic School uniform, and Homura mentions having gone to a Catholic school in episode one. It's very possible that Christianity spread through Japan much more thoroughly in the world of PMMM than in our world, perhaps through some wish. (Maybe even Kyoko's...)
 * Mitakihara's chief religion is Kyoko's father's cult.

Roberta as a regular girl...
...was isolated due to being very bitter and dislikeable, and maybe even snobby and prideful. So she filled her head with fantasies of the people who disliked her, only instead they worshiped her. Her wish made this dream a reality, hence the nature of her familiars and Roberta found that having her ego stroked was not as she had hoped it would be, (possibly due to clinginess or jealousy of others) so she fell into despair (which may have involved alcohol as well) and, well, the rest is history.

Jack the ripper was the result of a witch.
As this troper can recall, Mami notes that both unexplained suicides and murders can be attributed to a witch's kiss. My theory is that whoever the killer was lost part of his soul and killed people to "make it whole" again. Or it just be the witch manipulating him directly.

All the familiars to Witches were people, victims, converted into that.
In the first time line we see from our perspective she begins witching out on one, maybe two, guys on the train. Her familiars are a legion of men who look performing just for her. In the flash back timeline we see a different familiar, perhaps in that timeline it wasn't two smucks she takes but Hitomi.
 * Word of God said she didn't kill anyone in the anime.

The plot of the sequel movie will be the What Could Have Been from the Drama CDs.
Based on Shinbo calling it "Incubator's Counterattack".

Roberta is Madoka's teacher, Kazuko Saotome.
In one of the timelines in Episode 10, the girls are shown battling Roberta, the Birdcage Witch. There seems to be evidence that Roberta is the witch form of Madoka, Sayaka and Homura's teacher.
 * Roberta lives inside a birdcage. What do the classrooms in the girls' school look like? The birdcage can also symbolize the loneliness Kazuko experiences due to her constant rejections.
 * Pretty much every time Kazuko is shown in the classroom, she is almost comically furious at dates of hers who treat her in ways she feels are derogatory. Now look at this part of Roberta's description: She continuously stamps her feet inside her cage, directing her rage at those who do not respond to her.
 * Roberta is also associated with alcohol. In Episode 11, we see Kazuko and Madoka's mother in a bar together. The familiar manner they have and the sensitive topics they discuss clearly show them to be good friends, and since Madoka's mom almost always has some sort of liquor with her, it's not improbable to assume the two of them are or have been drinking buddies. In addition, alcohol is typically something adults consume on dates - dates like the ones that cause Kazuko so much stress.
 * Roberta's familiar, Gotz, is described as such: These birds that swarm together are idiotic men. Even though they are total good-for-nothings, they try to attract her attention by swarming around her feet and attempting to woo her. They are nothing more than an object of disgust to the witch. If a witch tries using her barrier to live out her fantasies; as seen by Octavia's concert hall, Gertrud's garden, and Charlotte's world of sweets; it fits that the emotional, easily angered Kazuko would get a kick out of reducing the men who rejected her to meaningless idiots who clamor for her affection. She is disgusted by them for disrespecting her.
 * Finally, we have a production note describing Roberta: A witch who lived for a long time as a magical girl. She is weak, as she was no longer a girl when she became a witch (mid-20s to 30s?). The form she takes in her barrier is how she would've turned out in the future (around 40s). What she desires is life. Enjoys alcohol and books. Kazuko is no girl, she likes liquor, as a teacher she is obviously going to like books, and all she wants is a life with a man who can appreciate her.
 * The biggest problem with this theory is that Kazuko is probably not a magical girl in the "current" timeline, which can possibly be handwaved by Homura's game with the Timey Wimey Ball.

The new girls from the mobile game have nothing to do with the witches in-show.
We keep guessing and assuming this girl is that witch, and it never comes to fruition. So, let's jump the gun!
 * In an actual WMG, while Komachi and Claire may in fact be Elly/Kirsten and Elsa Maria, Elise might not have anything to do with Walpurgisnacht despite having physical similarities (and I can't think of who Hiyori could be at all).

Homura's Hammerspace power isn't Hammerspace at all.
Think about it. Homura's wish gave her the power to screw around with one month's worth of time. It doesn't really make sense that it would also give her an infinite amount of storage space that takes up no actual space. However, where does she put these weapons when she's storing them away? Behind her shield. AKA her time machine. She's not actually storing them, she's sending them directly to the point in the future when she'll need them. And how does she know when that is? At the time, she doesn't; however, when the time comes, she always reaches behind her shield to retrieve the item she needs, so she could in fact be reaching into the point in the past (which she does know) when she "stored" the item in the first place, thus taking it directly out of her own hands.
 * On the other hand, Hammerspace can come with the Time Master package. TARDIS anyone?

Theories why Madoka could see Homura fighting Walpurgis Night (both in the show's timeline and the one immediately before), despite not being a Magical Girl (yet)

 * Madoka's magical potential was so great that it qualified her to see Walpurgis even before she used it.
 * Kyuubey allowed her to see Walpurgis, possibly to encourage her to become a Magical Girl.
 * She couldn't actually see Walpurgis, but she had been told about it, and when she saw Homura getting smacked around and buildings thrown at her, she knew what was responsible.
 * Actually, we know the reason, and it's none of the above; Kyubey allows girls he intends to contract see himself and Witches, just like he helps transmit their telepathic messages.

Theories why Homura could never defeat Walpurgis Night by herself, no matter how hard she tried or powerful she became

 * Madoka became more powerful with each iteration of the time loop because she was the sole cause of Homura reversing time. However, whenever Madoka died or became a witch, it was usually because of Walpurgis, making it the indirect cause of Homura reversing time. Thus, Walpurgis also became more powerful each time, going from two ordinary Magical Girls being able to defeat it to an extremely experienced Magical Girl with tons of firepower giving it her all being unable to scratch it. The hyper-charged Madoka was the only one who could have possibly stopped it.
 * Walpurgis Night is immune to all non-magical damage, and none of Homura's weapons are magical. She was only ever able to defeat it with Madoka's help.
 * Walpurgis Night is a Puzzle Boss that can't die until it has been damaged by at least two Magical Girls—Mami and Madoka in the original timeline, and Homura and Madoka in most of the others.
 * In the Final Fantasy series, there's a type of recurring monster called a Tonberry, which usually has a special attack that does damage based on the number of monsters the target has killed. Walpurgis might have a similar ability: rather than dealing more damage based on the number of witches her opponent has killed, though, I think it might be that her strength is tied to the number of Magical Girls/witches her opponent has seen die in their life, rather than the number they've directly killed. Going by the five timelines we've actually seen:
 * Timeline 1: Mami dies against Walpurgis, and Madoka wins with a suicide attack. Since this is before Homura started those time loops, Madoka would only be as strong as a normal Magical Girl, so why would she, who's only been at it for less than a month, be able to succeed even at the cost of her life where Mami, a powerful veteran with years of experience, could not? The answer: Mami's seen a lot more witches die, of course.
 * Timeline 2: Madoka would have seen the same number of witches/MGs die as the previous timeline, but she's able to survive here because Homura is with her, along with the magical power boost from the first timeline. Homura gets through this battle more or less fine.
 * Timeline 3: Madoka would have seen the same number of witches/MGs die, again, with a couple of additions because of the Sayaka/Kyouko bit. Homura now has a few timelines of deaths under her belt. Even with Madoka's time loop power boost, both girls are completely drained in the aftermath of the battle and can't even sit up.
 * Timeline 4: Homura's seen even more deaths by this point, especially if she really did take out every single with in this timeline by herself. Despite several timelines' worth of experience, though, she doesn't manage to inflict much damage and gets taken out of the fight fairly easily. Madoka proceeds to win in one attack (while this could simply be a result of her insane power from all the connected timelines, it's also possible that this was helped by the fact that the Madoka of this timeline was unaware of Magical Girls and witches until right then, and so Walpurgis had little power against her and little defense against her already overwhelming attack). Afterwards, Homura is still able to get up and walk away, though.
 * Current timeline: As always, Homura's seen even more death. This time, we can see quite clearly that Walpurgis is almost completely unfazed by Homura's attacks, and Homura herself ends up beaten, bloody, and with her leg pinned under rubble, giving in to despair without having landed a single effective blow.
 * It's not a perfect fit, I know, since Madoka's successes can easily be attributed to Homura's timehax unwittingly supercharging her magical potential, but it does offer an explanation of why even an experienced Magical Girl like Mami wasn't able to do much, and also why Homura seems to be doing worse in every timeline, even though she should be getting stronger every time.

== Kyubey lied about the entropy part. Throughout the entire universe there are more effective ways to harvest energy and overcome entropy (the universe is big, what do you expect), but it's just because for him personally magical girl souls taste better and/or is basically drugs to him. == In this case he's more like the C'tan. Also fits in with "Kyubey = deceptive soul-consuming Eldritch Abomination" speculah.
 * When you take too much drugs, you become dependent on it, and when you decide to suddenly abstain from it, you suffer decay and loss of energy. Entropy, From a Certain Point of View.
 * Unfortunately for him Madokami, who was supposed to be today's special, screwed his dining system, forcing him to eat either horrible-tasting alternative energy resources or slightly less horrible-tasting demons for the rest of eternity.
 * Alternatively, the Madokamistic system is less potent, but with less devastating withdrawal symptoms. Perhaps similar to your daily cup of coffee or nicotine gum replacing cocaine and tobacco.

Madoka isn't done resetting the world yet
Okay so Magical Girls don't turn into witches any more. But they still have to fight, and eventually die/dissapear. That's not really a happy ending. But Madoka was a bit pressed for time. She could only come up with so good a wish. However she's got more to her plan. Okay in the new universe the Magical Girls fight Demons right? Demons live in hell. Madoka takes the magical girls to heaven/Valhalla. the inhabitants of hell are opposed by the inhabitants of heaven. When the Ragnarok/final battle against the demons rolls around, and their leader/supreme demon/the devil/Incubator/whatever appears, and it apears all hope is lost, the sky will split open. And Madokami will appear with every magical girl who has ever been, will ever be, or could ever be. Only now they'll all be goddess like Madoka. And they will make it so their is a true happy ending.

Madoka is the temporal equivalent of a black hole.
Homura's repeated time travel causes multiple timelines/universes to converge onto Madoka. The timelines reach the temporal equivalent of a critical mass. When the last trigger is used (Kyubey unlocking her potential) she then transcends the critical mass, absorbs the entire spacetime continuum into herself and proceeds to fuck up reality as we know it.

It's not completely Sayaka's fault that she became a witch in every timeline.
Sayaka has an extremely self-destructive nature, as evinced by her dying even in the witchless world. But she only died every single time because Kyubey was intentionally targeting her. Kyubey's only goal is to get Madoka to make a contract. Two possible paths to that are to torment her friends enough for Madoka to make a wish to end their suffering, or to make Walpurgis unbeatable without Madoka's intervention. If Sayaka becomes a witch, Sayaka herself is out of the picture and it also makes Kyouko very likely to die. If Mami is still around, the Puella -> Witch revelation will drive her to murder all her comrades (and probably attempt suicide afterwards). Even setting Sayaka on such a self-destructive path is enough, since in the series Madoka tried to contract to reverse it. So, taking a few minutes to have a private conversation with Sayaka about how she doesn't have to feel pain is one of Kyubey's most effective tools to discreetly force Madoka to contract without making his malicious nature obvious.

Kyubey isn't eating Grief Seeds.
He gains energy just from the natural process of magical girls turning into witches or maybe from the existence of magical girls fighting witches, not from the physical Grief Seeds themselves. He doesn't need them, but he takes them from the magical girls anyway so he can plant the seed and have a witch come back faster. That opening in his back leads to extra dimensional storage or a hollow interior or something, unlike his mouth, which he's been seen eating out of. Otherwise, his desire to contract Madoka doesn't make sense, because no one would ever be able to defeat Gretchen and her Grief Seed would be unreachable.

The original wish of Walpurgis Night before becoming a magical girl in the first place
was to become better than everyone around her. So every time a newcomer arrives and show a special talent, that girl will automatically assimilate that skill, but better. Then everyone becomes suspicious and that becomes her Start of Darkness. Her witch form reflect her wish by assimilating in everyone nearby (hence Walpurgis Night as a gathering of witches) and making familiars out of them.

Charlotte is Kyouko
In a, Kyouko was addicted to sweets and cheese and became a ]  She still pigs out on treats at times, but, attempts to stay healthy and eats apples, because she was unhealthy in her  , and, while she cannot remember that, she feels guilt eating too much junk.

There were mahou shounen, but someone wished them out of existence.
How and why? Who knows. Maybe they bought Kyubey's spiel about entropy, but wanted to save all their magical friends, who happened to be boys. Maybe they thought girls were better suited to be sacrifices. Maybe they thought girls were better suited to be heroes. Maybe they wanted girls to have magical power to balance their lack of societal power. Whatever the reason, someone said something along the lines of "I wish girls are, were, and have been the only suitable candidates for contracting". Maybe they even said "I wish everyone who ever contracted was a girl".

The original Moemura still exists in every timeline and is witnessing everything Homura does in every timeline after the first.
Homura's time travel powers aren't Mental Time Travel - she just sends her soul gem back. Since her soul gem is her true self and contains her consciousness and powers, it's essentially the same as Mental Time Travel while keeping her contract valid. She travels back to the 16th on the day she's going to be discharged from the hospital, ending up in the hands of her former body.

Normally, this body is just hardware, but there's already a consciousness in that body... no matter, though, because Homura's stronger than her former self and can just hijack the body. In theory, her soul gem being over 100 metres from her body wouldn't result in death-like symptoms, as her old self would regain control.

Possibly not valid in the Godoka timeline because of her new powers, though.

The Incubators are an insect-like society.
On their home planet, they live in hives, possibly "ruled" by Incubator Queens. Their ideas about the worthlessness of the individual before the common good hints strongly towards this.

H.N. Elly/Kirsten was actually an extremely powerful witch.
She has kissed a huge amount of victims, enough to form a whole ritual suicide cult - a feat not repeated by any witch seen before or after. The reason why she was killed easily by Sayaka is because she had expanded all of her energy on Kisses to form said death cult.

This takes place After the End
The theory is too long for this page, so here's the link to it and first paragraph. This theory makes even more sense after ep.6.
 * http://wiki.puella-magi.net/Speculah:Pillar_System_Theory
 * Once upon a time no longer, the "Real World" collapsed. The result was a void in which even "time" and "space" couldn't exist as concepts, and the only existences that persisted were souls. Some souls were stronger than others; their dreams and desires imposed themselves on the nonsubstance of the void, and became bubbles of newborn "reality." These bubbles were called Labyrinths, and their creators were called Witches.

Becoming a god-like being is a "natural" ability of Puella Magi because they're liches.
In Dungeons and Dragons, by separating their souls from their body; Liches gain power; which they use to study to become the next level. From Lich to Demi-Lich to Arch-Lich to Deity. Puella Magi are "partial" Liches, however, since Kyubey is draining crucial energy needed to maintain their focus. "Witches" are a kind of failed Demi-Lich transformation; they only partially achieve an astral state and are still fused with their damaged phylactery/grief seed. Madoka jumped several levels with her wish and succeeded in becoming a God.

Puella Magi "sidestep" entropy because they generate equal amounts of positive and negative energy.
"Hope" and "Despair" in equal proportions cancel each other out mathematically. Thus equal amounts can be created and still maintain the equation; like virtual particles; but on a larger, magical scale.

The magical system DOES NOT actually add energy to the universe (which violates the Equivalent Exchange theme).....
What the magic is doing is healing the universe; the inevitable increase in entropy is rotting it. Energy is changing form without overall increasing or decreasing, as outlined by the First Law of Thermodynamics (Equivalent Exchange); according the Second Law of Thermodynamics (Entropy), it will never be a 100% perfect conversion into work, with some energy changing from being localized to randomly dispersed (mostly as waste heat). It might make more sense if you replace "the universe is losing energy" with "the universe is ageing/decaying/degenerating until it becomes too old and inefficient to sustain life" (which is pretty much what the Heat Death is about), and "adding more energy" to "the souls of magical girls (who can of course symbolize youth and fertility) reverse the process of energy decay, returning energy to a better, less entropic form, and provide some sort of Philosopher's Stone for this universe in order to rejuvenate itself".

The Puella Magi system sidesteps physics by absorbing/converting physical energy into a psychic equivalent
Despair (represented by Witches and Daemons) is basically the emotional equivalent of accumulated Entropy. And Incubator tech can be presumed to be sufficiently advanced enough to create life-energy based power plants ala Mako reactors. Somehow the Puella Magi/Witch cycle absorbs entropy from its surroundings (like a metaphysical air conditioner, but instead of simply and inefficiently shunting entropy outside, it reverses the "Energy of all types changes from being localized to becoming dispersed or spread out, if it is not hindered from doing so, usually as random heat" thing which is basically what the Second Law of Thermodynamics aka Entropy is about), and condenses the physical process of entropy into whatever mysterious-yet-far-more-useful form of psionics that the Incubators would then harvest to feed into themselves and the physical universe.
 * If sufficient despair/entropy is absorbed and put back into a localized singularity (you know, like black holes) it could theoretically create a Big Bang, hence Madoka's potential enhanced by Homuhomu piling up multiple fate lines (and thus desperation) unto her.

The "entropy" Kyubey referred to isn't Thermodynamics, but an Eldritch Abomination.
Said Abomination exists outside of the universe, is even more alien than the Incubators themselves, infinitely worse than our limited scientific conception of entropy, and is eating Reality alive. Because of its true form being just plain Inconceivable, the Incubators can only describe it vaguely by making parallels with the scientific entropy we learned from ordinary middle school Science (hence why they refer to it as Entropy, thus this Abomination is basically Entropy From a Certain Point of View, with the Incubators being pathological users of From a Certain Point of View). The Incubators became an emotionless Hive Mind Singularity in an attempt to preserve their civilization from such an insanity while increasing their collective intelligence enough to know just a subatomically small bit of it, only for them to discover that almost every scientifically-based means in the universe is not enough to stop it.... except for a certain form of energy on which they themselves can't even comprehend why it works anyway out of all things. The necessity for tormented girls' souls to be sacrificed to it in order to stave it off? Same thing as to why the Dark Eldar sacrifice tortured souls to Chaos (another name for Entropy) so that it does not eat them alive instead. Fits in with how a Cosmic Horror Story will always have its hierarchy of abominations to be Always Bigger And More Inconceivably Insane Fishes.
 * It gets worse. Think with Madokami-sama around we are finally saved from such? Yes, Entropy seems to have slowed down its role in Reality for a bit while relatively less-entropic Daemons seem to have compensated for its role on the world.... because Madokami's immortal potential has provided it an all-you-can-eat buffet of energy, and in exchange for our Salvation it is Her that is being eaten alive slowly and painfully instead, at every point in space and time, with no way to undo or escape, as long as the mere concept of Existence itself continues to exist, forever and ever.
 * And that eldritch horror is, of all things, You.....

Earth and other emotionally-ridden worlds also have a double purpose of being asylums for mentally-ill Incubators.
Among Incubators themselves emotion is a mental disorder, but you need to have an experience of having a little bit of emotions themselves to know how they affect an organism (and thus harvest Puella Magi). Thus, those who have a little bit of emotion (like Kyubey) are instead sent on Puella Magi-hunting sessions which also banishes them from Incubator society-at-large at the same time.

Suleika was originally a Ninja Puella Magi
She thought it would be an awesome thing. She was wrong. Hence, the delusional nature.

Some other Witch theories...
(From the messageboards) Amelia Earhart manifested herself as the Bermuda Triangle (or one of several other "vortex zones" throughout the world). The crew of the MV Joyita may have fallen into one of them (especially since Amelia disappeared in the Pacific, not the Atlantic). In keeping with Gratuitous German Theme Naming of the Witches, let's call her form "Ehrhardt".
 * Marilyn Monroe committed suicide after she vainly tried to seduce John F. Kennedy. About a year after her death, she formed a barrier around Dealey Plaza in Dallas which not only murdered Kennedy but also generated images of multiple suspects (Oswald, the guys behind the grassy knoll, the tramps, etc.), hence the lingering mystery.
 * She was also probably behind the "Kennedy Curse" (Robert Kennedy's assassin Sirhan Sirhan claimed he was in a sort of "trancelike state" when he shot Bobby.)
 * Roberta may be her Witch form.
 * Janis Joplin murdered Jimi Hendrix (who was 27 at the time) in a fit of despair in her last month of life, much like Sayaka possibly murdered those two misogynists on the train. After becoming a Witch herself (at age 27), she began the 27-year curse which of course later took Jim Morrison (who was a possible one-night stand lover of hers) and later Nirvana Kurt Cobain and Amy Winehouse.
 * One of Osama Bin Laden's wives. She was already "weakened" and developed a dislike for the West as a child in Soviet-occupied Afghanistan, and wished for the Soviets to be removed from her country. Osama "picked her up" if you will while a mujahideen "freedom fighter". His horrific abuse of her (remember, this guy used some of his wives as Human Shields) coupled with fundamentalist zealotry pushed her over the edge sometime before 2001. As a Witch she eventually kissed him...I think you can tell where this is going.
 * With Haiti's Woobielicious history of slavery, dictatorial rule, genocide and horrific poverty, it proved a very fertile target for the Incubators. Add Hollywood Voodoo to that and, many years later, you get the 2010 Haiti earthquake, which may have been brought on by Walpurgisnacht herself like Japan's quake a year later. Hurricane Katrina may have had similar origins, as Louisiana has a somewhat similar history (and many slaves from there and Haiti were probably bounced between the two while both were still French colonies).
 * You know who else fell on Walpurgis Night?
 * No wonder Walpurgis Night was so powerful: she was born from a massive reservoir of complete misery and hell.
 * You know who else was the centre of repeated time travel and failed assassination attempts?
 * Theory: Originally, Walpurgis Nacht despite being a collection of witches was in itself started out as fairly ordinary, but over time it continued to assimilate misery into itself, thus it got supercharged to insane levels when the World Wars came to sacrifice people by the hundred millions to create a massive reservoir of miserable souls in just a short amount of time, which unlike other apocalypses like the Black Death was entirely caused by the energy of human rage (perhaps with a heaping help from possible Nazi Alchemy experiments, and of course how the opportunistic Incubators took this as a time to contract war victims such as Anne Frank, most of whom are so desperate they couldn't think of simply ending the war and made selfish wishes, or they can't stop it because the World Wars is so full of misery only a Madoka-scale wish can undo it). On April 30, aka Walpurgis Night and the day Adolf Hitler committed suicide, Walpurgisnacht reached critical mass when it assimilated the soul of Hitler who contained extreme amounts of rage that rivals the energy of a Magical Girl (for the Despair Event Horizon part, just see Der Untergang), enabling it to transform into something capable of singlehandedly bringing the Apocalypse (well at least it slept until Madoka got the contract). Also, according to Word of God, Walpurgis wants to turn the world into a stage. Hitler had such a massive fond of Richard Wagner's epic operas that he probably imagined himself to be in it, seeing his Downfall as Gotterdammerung.
 * Or Hitler was simply just a victim of a suicide-inducing kiss courtesy of Walpurgisnacht.
 * As for the trope called Hitler's Time Travel Exemption Act, they're extensions of Homura. When you kill Hitler things get worse, when you try to stop Walpurgis things get worse.....
 * Salvador Dali saw one of the witches and its barriers early in his life and was inflicted with both inspiration and insanity, leading to his fame as an eccentric artist. Tell me that his art doesn't look like it came from Witches' barriers.
 * Witches also influenced most of 20th century art and literature, from the weird styles of the Dada to the Eldritch stories of H.P. Lovecraft.
 * Speaking of Lovecraft, the Salem Witch Trials of course created Witches rather than destroyed them. H.P. encountered some of them, and The Cthulhu Mythos and all the rest were the result. (Fictional Arkham, Massachusetts is after all not far from real-life Salem.)
 * The cursed Indian Burial Ground in Pet Sematary is the barrier of a Witch who was an Native American woman. She contracted with an Incubator after her child died of smallpox introduced by the arriving colonists, and wished for her child to return from the dead. The resulting zombies are her familiars, and the Wendigo that Louis Creed sees in the woods is her Witch form.
 * It should be noted that Gen Urobochi has cited Stephen King as one of his main influences.
 * Room 1408 of New York's Dolphin Hotel was formed when a poor Irish immigrant wished her children could rise above her impoverished situation. One of her sons did...by starting a real estate development agency that eventually bought out her property to build the hotel. And now of course one of the rooms on the 13th floor (labeled as the 14th) is her barrier, and guests have a tendency to "check out" without ever leaving.

Madoka not only reformed the system, but saved the incubators.
The idea of extending the lifespan of the universe sounds good. But if the universe itself has a natural life cycle (like a gigantic cell), then what the incubators were doing was staving off apoptosis by artificially inducing telomeres to keep the universe itself long lived. Unfortunately, the Incubators failed to realize (or just didn't care about) was the fact that this would also turn it into a cosmic cancer, which could metastasize and infect other universes. What happened was that other universes made subtle changes so that the corruption would stay contained away from their universe, but didn't expect Madoka to turn it into a symbiotic system.

The backgrounds during the Transformation Sequences is actually a mini-barrier.
From the outside it appears as a brief glow coating the girl, but inside is a small bit of compressed space where the girls suit up which, like any good Pocket Dimension, is bigger on the inside. This is a subtle hint as to.

Kyubey is actually a witch.
With few exceptions, runes have only popped up in two places: within a witch's barrier... and within Kyubey's Mind Rape in episode 11. Since the runes seem to be a product of magic (the exceptions appear in places touched by magic, either witch or magical girl), which is a complete Black Box to the Incubators, it only makes sense that Kyubey is in some way magical. And he's no magical girl.

He is the witch of creation with a calculating nature. It is his job to maintain the existence of witches by forming contracts with mortal girls to turn them into magical girls, the child form of witches. As essentially the queen ant of all witchdom, he takes this responsibility very seriously, and comes up with any number of plans to ensure witches will always populate the world. This means he's either a Mother of a Thousand Young or a Monster Progenitor; personally, I'm leaning towards the latter.

Kyubey is likely the absolutely most powerful witch ever ; like Walpurgisnacht, he doesn't have a barrier, but unlike her, he's so strong he doesn't have to impose barrier-like qualities on the world around him in order to maintain his existence (except maybe enough for him to teleport around like he did in episode 9). That's not to say he doesn't have a barrier; he has one, but he is in full control of how, when, and for how long it manifests. What we see in episode 11 is in fact Kyubey temporarily forming his barrier around Madoka. Hell, he may even have been powerful enough.

It's quite likely he was even the very first witch on Earth. The ability to be Invisible to Normals is shared by all witches and familiars as well as Kyubey; theoretically, if a witch wanted to appear before humans, she damn well could, it's just more convenient not to so they can kiss them. Kyubey, however, is such a powerful and old witch, as well as the "mother" of them all in some form or another, that he can not only make himself visible to any mortal of his choice, but force all other witches to appear to those people as well whether they like it or not. Like other WMGs above, his "eating" Grief Seeds is actually a form of storage for them to be transported elsewhere and start anew.

As to the Starfish Alien and entropy story, he's either making it up as part of his plans for more witches or he actually believes that's the truth for some reason. Maybe it has something to do with his wish...?

== The ending is actually Homura's Dying Dream as Madokami hugs her (and everyone else on this cruel, cold world) and turns them into Morning Rescue. ==

Madoka didn't specifically wish to be able to travel through time, and we know Kyubey is pretty insistent on reading the fine print. So the only way she could remove M Gs' growing despair was to remove their AT Fields. Of course, that also necessitated removing everyone else's (including her own), so all of humanity got Tanged Morning Rescued. And of course it was just so much easier to suck energy out of a sea of orange soup than out of sentient beings.

So Congratulations, Madoka! Now if you would be so kind, please join Unit 01 forever drifting through space rather than leaving an eight-mile-tall rotting corpse for Shinji and Asuka to clean up.
 * Remember that Madoka is practically the Spiritual Successor to Evangelion. Knowing Urobutcher's penchant for It Got Worse, this will probably be the ending of the upcoming movies. Anyone got a shotgun?

Kazuko deliberately gave Homura overly hard math problems on her first day as a prank

 * She knew Homura would be behind on school work but wouldn't know how much, and so decided to make her feel even more out of place by giving her college-level math problems. Little did she know that after traveling through so many loops, Homura knows how to do the math (or at the very least, memorized the answers). Kazuko's tendency to do this might be one reason why she keeps getting fired from her teaching jobs.

Madoka had multiple wishes granted all at the same time because of how powerful she is

 * We know from Sayaka's contracting scene that one does not need to verbalize one's wish. While Madoka was making her huge Earthshattering Kaboom wish, she thought back to Mami's sacrifice and wished she could see her one last time. She thought of Kyoko's insistence that Madoka didn't need to become a magical girl and wished for her forgiveness. She thought of the life she was giving up and wanted to have something to remember it by. And she still really wanted that cake. All of these other wishes come true in the scene in Mami's apartment.

Charlotte was inspired by the Greedy's scene in Raggedy Ann and Andy A Musical Adventure.
Studio Shaft loves its artsy Deranged Animation, so likely some of the crew has some appreciation for underappreciated (and equally deranged) animator Richard Williams. Also, both creatures obviously live in worlds of desserts, both can "never get enough", and both are constantly trying to get one treat out of their reach (respectively, cheese and a "Sweet Heart").
 * By the same token, the Greedy could be another Witch, or perhaps an earlier form of Charlotte.

Witches (or something even more inconceivable) have always been Humanity's true form.
For some reason, we got Sealed Inside a Person Shaped Can, and the Incubators are one of the only things managing to unlock us.

The Incubators farm souls to avert entropy because they do not want to die
I always found Kyubey's motivations kind of suspect. He says he is trying to save the universe, but expresses little concern when a planet is consumed by a witch. The magical girl system itself is inherently unstable and will always result in the destruction of whatever planet is it used on.

Considering that they have conquered personal death, I believe that the Incubators are concerned solely with their own survival and consider any atrocity justifiable in order to maintain it. This only makes them evil from the perspective of their victims... wouldn't we do the exact same thing in their position?

"You have some really great ideas. I can make any of them true. All I need is for you to make a contract."

- /人◕ ‿‿ ◕人\