Shadow of the Colossus/WMG

Wander is the horned baby at the end.
Wander sprouts horns near the end, and then turns into a Colossus, but it's implied that he may be able to someday atone for his sins. This may stretch believability in terms of how quickly it could happen (or if he survived the temples collapse), but at the end, Mono finds a baby, with horns. That mostly reminds me of the ending of Terranigma. Think about it. It could be Wander! Maybe. Feel free to Joss me if you know something I don't.
 * Isn't that what most people assume?

The Colossi were magical guardians of Dormin's soul fragments
The hypothesis is that the Colossi were autonomous beings that had fragments of Dormin's soul sealed inside them (as 'living' Soul Jars) by, for example, Lord Emon. The idea was that no one could defeat them without the magical sword. I'm not sure which came first - the idols or the Colossi - but judging from what Dormin said, I'd say the idols came first and the Colossi were magically created by Emon afterwards.

"Dormin: The colossi are the incarnations of those idols."

Oh, and the sword was Emon's. It was instrumental in creating the Colossi, hence its significance in defeating them. It may have also been instrumental in forming the bridge to the Shrine of Worship, explaining why the bridge collapses later, but I'll come to that.

Anyway, the Colossi are left behind and Emon declares the land as forbidden as an added precaution. Later, in a completely unrelated event, Mono is sacrificed for having 'a cursed fate'. Wander has heard about the alleged powers of Dormin from Emon warning him and, determined to bring her back, steals Emon's magic sword and rides her to the Forbidden Land, and we all know what happens next.

Dormin cannot resurrect bodies in their current form, with their soul divided. Unfortunately for the Colossi, Dormin then has Wander 'prove himself' by killing all sixteen guardians. Dormin's soul fragments need a vessel, and with each Colossus' magical weak points stabbed, a Colossus dies and the magic around it fails, enabling the soul to transfer to Wander as a temporary vehicle until all sixteen are reunited.

At the end, however, all sixteen, because of this bit-by-bit accumulation, are currently trapped in Wander's body. This is at least an improvement on each one being trapped in a nigh-invulnerable Colossus, but Wander is now the one guardian of the one soul of Dormin. If Wander dies, then the entire soul is free to exit. Enter Lord Emon, whose men kill Wander, unaware of what will happen when he dies. Though they saw the demolished idols, they never saw a Colossus die and so don't recognise the signs of 'de-souling'.

Wander goes through the 'de-souling' process the Colossi went through (spouting Black Blood, turning black), but this time the whole soul is released, not just a fragment, so it is now powerful enough to fuse with both the corpse and the black spirits and create a Colossus body of its own.

Emon's spell at the end is him using it as a last resort. Originally, he'd hoped to merely contain Dormin's soul with a moderate bit of magic, creating the Colossi and all that. But having seen it fail, this time he's taking no chances and has the sword, the pool, Dormin and Wander annihilated in one last destructive spell. It also means that any magic used by the sword will fail, hence why the bridge collapses.

So, essentials:
 * Emon defeats Dormin in some past encounter.
 * The Colossi idols were carved and their respective Colossi incarnations magically created by Emon to act as Soul Jars and to guard the sixteen fragments of Dormin's soul, thus preventing him from returning.
 * Though created, the Colossi were autonomous beings in their own right and not necessarily bound to Dormin. They just happened to work as ideal 'living' Soul Jars.
 * The sword was involved in their creation, hence its unique power.
 * Wander is exploited into destroying and collecting Dormin's soul fragments until he has them all.
 * Dormin is now powerful, but still trapped inside Wander, who has become a new Soul Jar for the complete soul. Dormin still cannot escape on their own.
 * Dormin's task is now easier: they wait for Wander to get killed, thus releasing Dormin's powerful united soul. Then they merge with both Wander's corpse and the black spirits to create a body of their own.

Mono was killed with the sword Wander has for most of the game.
The sword was originally Emon's. He had someone kill Mono with it. Wander stole the sword and, via the events of the game, Emon reclaims possession just in time to create the vortex and destroy not only the sword, but the pool, Dormin and (possibly) Wander. When the sword was destroyed, the magical bridge collapsed and Mono woke up. In fact, the magical bridge collapsed and Mono woke up because the sword was destroyed - it was magical and involved with both of them. The bridge had been constructed via magic spell induced by the sword. Mono's death had been done magically. Destroying the magical sword cancelled out all its magic, including Mono's death.

Wander is already dead. From now on, you're controlling Dormin. The baby at the end is a byproduct of Emon's spell.
Wander died the moment he was stabbed. He went through the same death sequence the Colossi did. The running figure you control both times in Controllable Helplessness is actually Dormin.

The baby is:
 * Neither of them, but was created as a byproduct of the spell. Mono was already revived and was just taking her time to wake up, perhaps because the spell itself takes a long time to act.
 * A side effect of Dormin's ability to revive dead souls gone awry when Dormin tried a last-ditch effort to free itself. Mono was revived and Wander was reincarnated as a newborn.
 * Dormin deliberately sacrificing themselves to protect Wander out of gratitude for their brief stint in a body by reviving Mono, but then incompletely applying the same spell to Wander before annihilation.

Mono is the Queen from Ico
It's about time someone added this theory.
 * Moreover, to become the Queen is the "cursed fate" that she was sacrificed to avert in the first place. But because you can't fight fate, some damn young fool goes ahead and has her resurrected by the friendly neighborhood demon, dooming her and a whole lot of other people in the process.

Conversely, Wander is Yorda's father.
No rule saying they both can't be at immortal or at least immortal-on-stealing bodies...

The forbidden lands where the colossi dwell is really Where the Wild Things Are.
In Maurice Sendak's story, a rule-breaking youth traveling to a faraway land populated by huge, hairy giants and swiftly conquering them... sounds familiar? If you're not convinced, look at the covers and tell me those monsters aren't related.

Wander was turning into a colossus
Look at him closely near the end of the game, specifically his head. There is a rune like mark on his forehead.
 * Makes sense, given that he was basically absorbing their essenses.
 * This is less "Wild Mass Guessing" and more "Freaking obvious if you've completed the game".

Dormin was a competitor deity for Wander's religion.
Dormin is a nature/resurrection god that's kind of a mix of Pan/Osirus/Mithra et al. There was a religious schism that caused his priests to seal him into giant statues and take up a new religion, with the sword as the key to breaking him out. At the end, Dormin is sealed into Wander, meaning he and his descendants (Ico included) are demigods. Hence the fertility god-like horns they all grow and the reason the witch wants them and they're ostracized from society.

Mono's sacrifice was an attempt to Screw Destiny from one of Dormin's rivals.
Related to the above WMG... After sealing Dormin up, many centuries passed, and a young girl named Mono went to see a priest or oracle about something. Dormin's rival detected she would have some relation to freeing Dormin, freaked out, and had her killed. He/She/They just didn't see that Wander would gum up the works, possibly due to Blue and Orange Morality and thus being unable to understand just how far mortals will go for love.

The culture that built the structures in the Forbidden Lands was wiped out by Wander's people an extremely long time ago.
The people there were destroyed when Wander's people sealed Dormin, whose power sustained them and the land itself. There are lots of ruins and structures around on the map, some of them with no immediately obvious practical use (the standing pillars and archways in the desert, for instance, or the water-gazebo things past the waterfall), but no real evidence that there was ever any farming going on (lots of individual fruit trees, but no orchards, for instance, or herd animals). It's possible that that culture, which doesn't seem to have even left anything that looks like simple houses, may have been some kind of nature-worshipping, peaceful society whose god watched over and protected them directly. It might explain why the sealing was even possible; they might have welcomed a foreign tribe coming to perform a ritual in honor of their native god and not known what it was really about until it was too late, and part of the reason Wander's people sealed off the Forbidden Lands is that they didn't know Dormin's power was so crucial to their lives. As far as they know, Dormin simply killed all his worshippers when it was sealed up just out of spite.
 * It is possible that there's simply no evidence remaining of agriculture and anything other than the big stone buildings. After battle damage, fire and centuries of erosion and the Colossi stomping around, you're not gonna find much unless you start digging. (ask any archaeologist)

Team Ico's new game, The Last Guardian, is a sequel to Shadow.
"Guardian" referring to the Colossi. The griffin is a baby Colossus, and the last one left as the newborn offspring of one of the Colossi from the first game. The boy is a trainee to Amon's group, notice that the clothes he wears are similar. So it's about a young shaman and a young Colossus.
 * It probably will be (that, or a prequel), much like Shadow of the Colossus was to Ico. The creature from The Last Guardian doesn't look like one of the colossi to me, though, since it actually looks like a living creature rather than an moving statue.

Out of all the colossi, Malus (the final one) was the only one that was downright evil.
I mean, his name literally means evil in latin. But if that isn't enough for you (and why would it be? Pretty much the point of this game was to make you question such labeling.) then consider this: all of the colossi were apparently trapped inside the Forbidden Lands. Malus was locked behind a door that could only be opened after all the other colossi were dead. What's the point in making such a thing when the whole place was pretty much a seal? Malus was unquestionably the most powerful of the colossi. My guess is that he became so arrogant that he came to believe he was Dormin or something, and began wreaking havoc rather then just attacking in self-defense or living in peace. Since he was so powerful, Lord Emon and his followers, or perhaps the Colossi themselves, sealed him away behind the door.
 * The name "Malus" (along with the other names most people use, like Cenobia, Pahalanx, etc.) all came from a message board and aren't official. And he was locked away simply because he was the most dangerous; None of the colossi seem to be sentient, and many of them are almost totally mindless. I don't think that any of them could be considered "evil", as they were just acting on pure instinct.
 * They are official. A list of the names was a Japanese preorder bonus.
 * What if it's not so much that he was evil but that he represented the most of "Dormin" that still remained in the land. Maybe this forbidden area is where the entity itself actually laired. When the Colossi were born their spiritual energy was likely torn from Dormin and cast loose, entering natural materials like rock and dirt (this entrance point is likely where the runes are on their body) and the beasts were born. But the final Colossi is the remnant of Dormin as he was in his final moments, an angry deity. This beast could represent the main body of his masculine, aggressive embodiment while most of the other Colossi are more representative of the feminine, passive embodiment.
 * I always imagined that each Colossus represented some part of Dormin; that perhaps they were leeching his power away slowly, becoming bigger the more he expressed what they represented - with Dormin's ultimate fate to be split into sixteen mindless, wandering statues. The smaller Colossi, perhaps, would represent passions, something a creature of logic had little use for; the vast Phalanx accepting the inevitability of defeat some form of wisdom, and so on. If so, that final, impossible figure that towers over a forgotten battlefield, bound and literally smoldering, is Dormin's hatred of those who did this to him.
 * If you look at Malus, it almost looks sorta like he's got shackles on, as well as being trapped by that thing around his waist, like... Half an Iron Maiden, makes it seem like he's being punished for something.

The ruins spread out everywhere are much older colossi.

 * After Wander kills a colossus, if you visit it later, it has begun to decay into what look more like old ruins than a dead colossus. Who's to say this is the first time Dormin has attempted to seek out the power to free himself and why should there only have been 16 colossi?
 * Dormin, the 16 Colossi and that tower of worship, it is thought, are all references to

Wander is a hunter by profession

 * This would explain why he is capable of firing arrows while riding at full gallop, but still fumbles with his sword play. He is simply trained in using the bow, and not the sword.

Wander comes from a pseudo-Mongolian culture

 * This would explain not only his mastery of the bow, but also his special connection to his horse and his horseback archery skills.

Wander isn't his real name.

 * So, we have Mono, Agro, Dormin, Lord Emon, and... Wander. His is the Odd Name Out. Why is that? Maybe it's because it's not a name at all, just an adopted pseudonym for a nameless person. Here's a guess why: he and everyone around him believes that the moment he took the Ancient Sword and ran off to free Dormin and revive Mono, he lost his right to his name for such a heinous act. It's another price he paid for the bargain with Dormin even before talking to the sealed god.
 * Possibly Jossed by the Japanese title, Wander and the Colossus.
 * The translation of the title is rough and debatable. It's very likely that it's actually supposed to translate to "The Wanderer and the Colossus". Same thing with the 'name' "Wander". Some people translated it as "Wanda" some as "Wander" and some as "Wanderer". It's likely intended as the third, but was conjugated incorrectly or something. If that's the case, the name is likely symbolic like "Link" is in the Legend of Zelda games. Link is literally the "link" between the player and the game itself, and is more of a filler name than anything, and that's likely the case with our wandering protaganist here, too.
 * I always assumed it was supposed to be "The Wanderer", like "The Man with no Name".
 * Almost certainly Jossed now that the PS 3 re-release is coming up. The official game site gives his name as "Wander" in Romanji.

Wander wasn't the only one who got possessed by the Dormin

 * Alright, Dormin is fairly obviously a dualistic god. It speaks with both male and female voices, refers to itself as "we", and is said to have dominion over life and death. When Wander defeats a Colossus, a black energy penetrates him, and a black figure is seen next to him before he wakes up. Lord Emon says they's the spirits of the dead (which is backed up by the shadow-men in Ico). Now, aside from the shadows, one other thing changes when Wander kills a colossus; there appears a white dove next to Mono's corpse. This is because she, like Wander, is being slowly possessed by the Dormin; except where he's being possessed by the death (and probably male) part of its spirit, Mono is being possessed by the life part (note how the doves respawn if you kill them). This is how Dormin does its resurrecting mojo; like it says in the beginning, the laws of mortals state that, once dead, they're dead, and Dormin can't mess with Da Rules. But, if they're actually immortal spirits, on account of being vessels of Dormin, there's nothing stopping them from living again. Being possessed by Death would probably prove fatal to Wander, but the Dormin could always revive him, once freed. Unfortunately, Wander ended up losing his physical body entirely, so he had to be completely reborn.
 * One emerging theory states that this Dormin-possessed Mono would later become the Shadow Queen we all know and love. There is a gap in the theory, where the horned boys aren't with her anymore, as the reborn Wander was with her at the ending of Shadow, but it further states that the Shadow Queen seeks the horned boys in order to gather all of the essence of the male part of Dormin, and once again live as one. Furthermore, since her body would be quite aged, she would enter Yorda's body along with the male Dormin.

Dormin was always planning on giving Wander his body back.
If Emon hadn't interfered, Dormin still would have possessed him, but then released him once they got the rest of their body out of him. The end sequence was the god-bits getting forcibly removed and dragging Wander with them - a bit like the difference between getting stabbed near the heart and open-heart surgery.

The Smokemen in ICO and the similar creatures in Shadow aren't the same things.
The Smokemen who haunt the castle in ICO are actual spirits of dead people. The similar things in Shadow are pieces of Dormin. Smokemen have horns and 'eyes' - Dormin's bits have neither. It's okay, even Emon confuses the two.

Gaius (the third colossus) is female.
Just look at it/her! No male would have that tiny of a waist. Not to mention its armor. After you break its armor, the chest plate looks like one of those shirts that slings over one shoulder. It can't be male.
 * You haven't watched much anime, have you? That aside, I assume that they're genderless, but if they do have gender, then sure, why not.

The Forbidden Land is Hueco Mundo.
Dormin is a Hollow that was split into sixteen smaller Hollows. A powerful Hollow can be composed of thousands of souls, and when Dormin was split, the souls he was composed of were split into sixteen soul-blobs, which later became the colossi when they merged with nature. The more souls a blob was composed of, the more power it had, and the higher it's "rank" was (#16 was the strongest, followed by #15, #14 etc.). The reason Dormin is the only Hollow in Hueco Mundo is because So TC takes place After the End. The temple is all that is left of Las Noches. The group of people that the Wanderer, Mono, and Emon belong to are the descendants of every Shinigami in Soul Society, who after defeating Aizen in a great war were stranded in Hueco Mundo and started a new society. After a couple of generations, something caused Shinigami to lose their powers, and by So TC, only one Zanpakuto remained: the Wanderer's sword. As for the existance of Agro, we know that there exists Hollow versions of small animals like lizards in Hueco Mundo (sound familiar?). Without Hollows to prey on them, it is not too farfetched to expect some of them to evolve to larger animals, like horses, eagles (eagles can sometimes be seen in The Forbidden Land) and the deer we see in the ending (in the Garden). Agro is a hollow who was tamed and may or may not be an Arrancar (to explain his lack of a bone mask).

The Colossus were at some point, mostly normal specimens of their respective species. Except for one thing:
They were all hard to kill. My theory is that, back when Dormin was free and powerful, there was a cult that wanted to get rid of him. So, through whatever process, they started using the Sword to seal away bits of Dormin, as the whole would be far to much for any one creature to take. A minotaur roaming the edge of the city, a prize bull, a loyal Knight, etc. They keep sealing all the pieces of Dormin's essence away, until they get to the last piece. The leader of the cult, presumably a very religious man, knows that he will go to his equivalent of Hell for what he has done to get rid of Dormin. So, in a moment of self-sacrifice, he uses the sword on himself, becoming the last Colossus, Grandis Supernis. Dormin's consciousness, along with the 16 transformed creatures, were then locked away inside the Forbidden Lands. The Sword would be passed on along with the history of the Cult, as would the tales of the Forbidden Lands. Until one night, when a young man would take the Sword to those lands once more...

Emon didn't re-seal Dormin, he just set them back.
Come on, you expect me to believe that, after the ridiculous lengths someone went to to create the Colossi seal, saying a few words over a magic sword is really going to keep Dormin down for very long?

The colossi were once human beings.
After each colossus is killed and the idol shatters, a shadow figure in the shape of a human appears. This is because each colossus was once a person, and the pieces of Dormin's soul were made animate by the spirit of the human being in question. Perhaps they were religious followers of Dormin that were killed by Emon as punishment for worshipping evil, or were used as living hosts for the broken parts of Dormin's soul. Or maybe they were individuals who, like Wander, tried to defeat the colossi for their own or Dormin's benefit and ended up being destroyed and possessed in the process (or both; that would explain why some are confined as if to prevent them from escape and others are able to roam freely). We see at the end of the game that when Dormin possesses Wander's body, he takes the shape of a colossus. It makes sense that a piece of Dormin's soul would transform other human bodies, too, just less powerful. Emon also refers to the black shadow people as the spirits of the dead, which wouldn't make sense unless the dead were human beings that were somehow trapped inside the colossi, because they appear only after the colossi idols are shattered.

Mono is part of Dormin's seal.
When a colossus is slain, not only is there a shadow-man over Wander, but there is a dove by Mono's body. Dormin never planned to revive her. Instead, they planned to put the female 'voice' (which is gone by the time he is released) into Mono and the male one into Wander. Dormin was meant to exist in two forms from the start, which is why it still refers to itself as 'we', even when it dropped the female-half of its voice in the larger, shadow body. Combining his light and dark aspects effectively hand-cuft them and confused their power.

Wander has supernatural powers of his own. Or else a Charles Atlas Superpower.
How else to explain Not the Fall That Kills You, Made of Iron and Soft Water? In-universe, I mean. Out of universe explanations can range from Hand Wave, They Just Didn't Care and You Fail Physics Forever to Art Major Physics, A Wizard Did It and World Building.

Wander is undead for most of the game.
He actually does die when those first tendrils enter his body from the first Colossus, and the between-boss light we see is the tunnel of light before death. Dormin's power is keeping his soul tied to his body, but it's not perfect with the god still sealed. This is why he seems to survive more and more ridiculous abuse as the game goes on - he's already dead, though he can be knocked out by things that should be fatal.

Mono is a bitch and her cursed fate was a Self Fulfilling Prophecy.
Starting from the theory that Mono is the queen from Ico, maybe she wasn't that likable of a person in the first place and Wander happened to have a blind crush on her. Going off on my own here, Her supposed cursed fate which Wander may or may not have been enlightened on, involved the return of an ancient demon, if Dormin is as really really really old as we are led to believe maybe the tales of his tyranny were exaggerated like many mouth to mouth tales were.

The Miracle Grow Wander Theory
As you know, the story closes with Mono and a Magically Created Horned Baby Wander trapped in the Forbidden Lands with a bunch of animals and Agro, who seems to be blessed/magical in someway, being able to survive that drop. In this theory, Mono finds a way past that barrier via something in the garden, then rides out with some of the animals. she spends several months taking care of Baby!Wander, who grows swiftly and remembers much of his past thanks to Dormin, who simply wished to parasite off his energy until They could exist independently of him and take over the world (or what ever it is that malevolent entities with god powers do). Eventually, after these months, his growth slows, as he has returned to the age he was when he started this whole mess, and they find a way out of the forbidden lands. Thus, he and Mono become the progenitors of the horned boys. Now, the line of horned boys eventually melds into a village being subjugated by a body-snatching remnant of Dormin, which recognizes the remnants within the horned boys (which according to Word of God are represented by the horns) and begins demanding them as sacrifices, thus giving us the premise of Ico. Upon killing the Queen, Ico unknowingly defeats Dormin for what is hopefully the last time, and the ensuing descendants of Wander's line will no longer bear the horns.

Emon DIDN'T seal away Dormin
A lot of these theories seem to state that Lord Emon, who appears to be old but not horrendously so (perhaps 50?), sealed away Dormin some point in the past. Possible though this may be, it seems more probable that a shaman somewhen in the past did the sealing, and stories have been passed down in Mono, Emon, and Wander's society for generations about Dormin and the shaman, as well as the sword and the position of shaman - which is currently held by Lord Emon. The sword is passed from shaman to shaman, but it is known of by all the people that make up this merry society of unknown size, explaining why Wander knew about Dormin, why he knew he needed the sword, and how he knew where to get it. It was probably used in ceremonies.

Mono's cursed fate was to be sacrificed
Making this an example of Self Fulfilling Prophecy.

is proof of Dormin's goodness
They prevented  from being fatal because They were, at best, True Neutral if not actually Good, and this was part of the repayment for Wander's releasing Them.

The collossi were at least partially corrupted by Dormin, causing them to hold back and to get themselves killed.
Ever notice that the collossi always fall for the same tricks? Even ones that a creature acting only on instinct would know how to counter (such as when yuo climb into the palm of the hand of one of them and it doesnt just squeeze). Each collossi may have been the physical incarnation of parts of Dormin, and as such, when they saw someone coming to kill them (read:release the fragments of Dormin they held) they let it happen so that they could be released and eventually reformed.

The colossi didn't exist (or weren't alive) until Wander came to the valley
When he places Mono's corpse on the altar, a lot of shadow creatures appear. He points the sword at them and they turn into smoke. Immediately after that, a lot of thunder strikes places far away in the valley. Perhaps this is the moment when the "souls of the dead" entered the colossi's bodies, getting released again when Wander killed each one of them.

Half of Pelagia's head is missing.
Those nobs at the top of his head are his teeth.

Wander will see Mono again...
But not in the current life. Mono is revived by Dormin at the end of the story, but Wander is still dead. What likely happens is that if Dormin are in fact benevolent and reincarnated Wander, they'd give a similar gift to Mono or her descendant. Mono goes on and continues her life, and her descendant grows up to be Yorda, while Wander grows up to be Ico. They remember absolutely nothing, but possess the same soul as their ancestors, and possibly half of Dormin's soul each. The Queen is Emon's descendant and is inheriting the quest to slay Dormin once and for all from her great grandfather, unaware of Dormin's intentions. This plot line will be explored in the next installment of the series, should it get made.

The Forbidden Land is across the ocean from The Queens Castle in Ico
As hinted by the game select screen in the PS 3 re-release and that the beach that  can be found in Shadow of the Colossus.