DC Universe/WMG

The reason Superboy Prime was a footnote in the Superman Museum was because he matured and became Superman.
After the events of Blackest Night, Superboy-Prime realizes his crimes and sets about becoming The Atoner. His new hero career follows something along the lines of the Secret Identity story and he manages to become the Earth's greatest hero. However, he is still all too aware of his sordid past and continues to be wracked with guilt throughout the years, making him more of careful and self-effacing of a Superman than his counterparts. When the government builds him the museum, they try to cover up his past crimes, thinking it would negatively impact the people's trust in Superman and the government that supports him. However, Superman insists that they include his past history in there, as both a reminder to himself and the populace that he is but a mortal with the same flaws as everyone else, as well as that he has done horrible things and is only now making for them. He sees it as a way to keep himself from getting out of hand again, as well as a way to remember all those who he harmed. The government reaches a compromise by putting the section about Superboy in the museum, but only as a footnote. In the far future, the facts have become a little scrambled from multiple retellings. As a result, Superman Prime is remembered both as the universe's greatest hero, and the unspeakable evil that inspired the Legion of Supervillains. As a result, he inspires both the Legion of Super-Heroes and the Legion of Supervillains, both groups looking at separate points of his history. The arrival of Superboy in the Superman museum of Earth-Prime is part of a Stable Time Loop that ensured this history.

Alternatively, Superboy Prime became every version of Superman ever.
Following the above, despite becoming The Atoner and a hero to Earth-Prime, Superman Prime felt that he still hasn't made up for his crimes. As he's practically immortal, he became a heroic version of the Time Trapper. Once gaining these powers, he used it to access every timeline. He uses his powers to reincarnate as all versions of Superman. In every version, his drive for redemption is manifested in their status as The Cape, though the original personality remains as a secret,split version. Legion of 3 Worlds was a Batman Gambit to get his young self back to Earth-Prime, where he could have his Heel Realization.

The Linda Danvers Supergirl is really the Supergirl of Earth-Prime integrated into the Post-Crisis Continuity
Linda was born on Earth Prime as the daughter of Fred Danvers and Sylvia Kent Danvers, the sister of Earth-Prime Clark Kent’s father Jerry Kent. As a result, she is technically Clark’s cousin. She was born with a metagene which would have given her fire angel powers that would allow her to fight alongside her cousin Superman as Supergirl. This explains why she had a similar name to Earth-1 Kara and why she was able to substitute for Silver Age Kara for some time. Sometime before the the Crisis On Infinite Earths, she and her parents were plucked from their native Earth and set on Earth-1 for some reason. At the time of the Crisis, Linda was too young to fight against the Anti-Monitor’s minions and therefore did not appear in the story. After the Crisis ended, Linda and her parents became continuity refugees like Power Girl and were integrated into the Post-Crisis continuity. However, since she was still destined to become a Supergirl, Matrix fused with her to awaken her fire angel powers. Perhaps part of the reason the fusion was achieved was because they were different versions of Supergirl and thus could potentially fold into one being when given the means via Matrix's shapeshifting powers. Now that Earth Prime has been restored, Linda will be rescued from Hell and find out why she and Power Girl were allowed to integrate individually alongside the native Supergirl as part of some convoluted Xanatos Gambit before heading back to her native continuity and dealing with her cousin Clark as well as Earth-Prime version of Earth-0 heroes.
 * The only reason Matrix was able to properly fuse with Twilight was because Molly was Supergirl of Earth 1198 along with her sister Jane. They were sent to Apokolips much like her cousin Kal-El in Superman: The Dark Side. Like Linda, they were also shunted to Earth-1 before the Crisis so they could survive the erasing of their reality.

The new Aquaman, Arthur Joseph Curry, is actually a time traveling version of Orin's son, Arthur Jr.
Sometime in the future, Arthur Jr. is resurrected. However, something happens to catapult him through time, leaving him to be found by Phillip Curry. Devastated by the death of his wife and premature son, Phillip adopts Arthurs as his own child. A little bit insane with grief, Phillip convinces both himself and Arthur that he is Arthur's real father, and Arthur is the boy that Elaine died giving birth to. As Arthur grows, Phillip also makes up the "mutagen" story as an explanation to Arthur's abilities. However, Phillip does allow Arthur to keep the one thing that the boy still remembers about his previous life: his name. Arthur grows up unaware of his true heritage, but still resembling his birth father. The Lady of the Lake's tale of his origins was also a lie, since something in the future depends on Arthur not knowing his true origin.
 * Apparently Arty Joe was an alternate universe version of Aquaman or Arthur Jr who got stranded on Earth-0 after Infinite Crisis.

Hub City went to pot after the Blue Beetle left because he left.
Hub City, stomping grounds for Blue Beetle Ted Kord in the Charlton comics, seemed like your usual comic book City of Adventure... but eventually, after DC picked up the company's characters, Ted packed up and headed off to Chicago and further successes. Then out comes the '87 O'Neil/Cowan Question series, where the Question is the only hero in a corrupt, crime-riddled, crumbling Hub City that makes Bludhaven look like Fawcett City. What happened? Well, seeing as Kord was head of a rather successful company (name varying through the years), taking it with him when he moved to Chicago likely wreaked havoc on Hub City's unemployment rates, local economy, and ultimately the crime rate.

Death Is Cheap because Death of the Endless is too nice for her own good

 * Come on, you know how good natured she is. You think she's ever gonna lift a finger to stop someone from genuinely coming back if they have half a chance? She just smiles and waves, as several Green Lanterns, most of the Flashes, Green Arrow, a few Spectre hosts, Superman, etc all breeze past the wrong way, doing nothing to stop them, unlike the more work-focused Deaths of most universes.
 * Alternately, she could just be secure in her job. "I'll take you eventually" is (somewhat) how she once worded it. Now, tomorrow, a hundred years, a million years, eventually, she will do her job. And she never said she minded having to do it more then once.
 * Alternately Alternately, maybe the heroes of the DCU fall more into Dream's domain? Much like Prez the teen president, when they die they are given the option of going to the Dreaming, from which Dream may allow them to return to life, because their stories aren't done yet.

Alternately, it could be several of The Endless indulging in sibling rivalry or appointing agents to enact their private agendas.

 * Destiny might not say much, or reveal what's in the book, but he is the eldest. Once someone has accepted the role of a costumed hero/villain, then the usual rules stop applying, they get marked by Destiny, and become witting or unwitting agents of the Endless. This applies to Hero and Villain alike because the Endless are Chaotic Neutral or True Neutral forces of the universe and the whole morality thing doesn't apply. Delirium likely holds dominion over Mxyzptlk, Bat-Mite, Ambush Bug, the Joker, the Question, and a wide variety of Silver Age crack. Delirium is also the most likely to let the ones under her control know they're being played, hence these characters treating the fourth wall like a minor annoyance...but since they ARE under her sway, no one's going to believe them anyway. Desire's probably having a field day with the Star Sapphires while hir twin's got Sinestro's gang covered (Reacting out of fear and trying to make anyone too afraid of you to fight? Yeah. That's doubling down on Despair). Despair probably also gets dibs on Doom Patrol. With Destruction's leave of absence, the costumed crowd fills in the gaps with the massive amounts of they deal in the fights...but I'd still say Destruction's got final say on folks like Darkseid and Deathstroke. Dream has the Blue Lanterns, and most of the REALLY driven Knight Templar and Well-Intentioned Extremist types. Like good siblings, they will occasionally share their "toys," or pit their toys against their siblings' toys. If Death takes one of her siblings' agents off the field, her siblings will find a way to "steal them back," leaving her in a never ending job. It's simpler to stick to "ordinary" mortals and let her siblings play with their action figures.

Alan Moore is God.
Have you seen the DCU's Abrahamic God? It's clearly Alan Moore, much in the same way the God of 616 is Jack Kirby.
 * And the recent crises are clear evidence of how "God" has abandoned the DCU.

Deadshot is HIV positive.
It was really weird that they would point out how he was smoking blood covered cigarettes. And it would put his whole "not giving a damn about living or dying" thing into perspective.
 * Isn't immunity to disease part of his power, as Required Secondary Power of his Healing Factor? Otherwise he would likely have died from massive infections years ago with all the deep wounds he's taken.
 * I don't think Deadshot has one of those. Is it possible you're thinking of Deathstroke?
 * D'oh!

Superboy-Prime is going to discover TV Tropes.
If Earth-Prime is essentially our Earth, then there is likely an iteration of this site there that he can access. Which will in turn cause him to have No Fourth Wall, granting him all the Genre Savvy he'll ever need to finally win. Think about it, if he can punch reality to effect a Cosmic Retcon, then maybe the fact that DCU keeps getting worse is a calculated effort on his part to produce a reality dark and cynical enough to allow a villain, which is what he's self-aware to know he is now, victory.
 * Alternately, he's trying to punch it better, and just doing a really, really crappy job at it.
 * I think he already has. Check the Poison Oak Epileptic Trees. One of the WMGs is that people in Real Life are complete monsters. As of Blackest Night, Prime calls out the writers. I think that WMG is due to Superboy-Prime knowing that fictional universes are real, and hating the fact we're blissfully unaware of this.

All those beings who alter reality are really storytellers, and The Multiverse is simply different people's attempts to tell the same stories.
Both "Legends of the Dark Knight" from Batman the Animated Series and Whatever Happened To The Caped Crusader? use the storyteller device to tell completely different stories about Batman...Perhaps what "really" happened has yet to be told...

Rex the Wonder Dog is the second coming of Jesus
Praise be unto Rex!

Krypton was the "human life" created by Doctor Manhattan
Deciding not to even bother with his own universe anymore, Doctor M. decides to use a relatively quiet little reality for his experiments. Naturally, given his entirely rotten luck, the planet goes boom, and, in a last-ditch effort to save his creation, he loads the dice and sends baby Kal-El's spaceship to Earth, the only planet he knows he'll be safe. The rest is history.
 * In this way, Alan Moore is the entire reason superheroes exist in the first place!

Captain Marvel doesn't really have the powers of seven gods-- Shazam just told him that to channel his powers in certain directions.
Come on, the first letters of all the beings' names (in English) just happen to spell the name of the millenia-old wizard (in English) when both the heroes named and said wizard lived and died long before English existed? No, it's more likely that CM's powers are far broader than what's shown, but Shazam told a little white lie to narrow down their focus and make him think he was more limited than he truly is; especially telling Billy that his powers included "the Wisdom of Solomon" specifically to give him that wisdom, or make him think he had it -- thus making CM too wise to repeat the mistakes of Black Adam.

Evidence? In The Golden Age of Comic Books, Captain Marvel was not just a Flying Brick, but often had New Powers As the Plot Demands, such as super-hypnosis-- powers which often made only a single or a handful of appearances, as he literally forgot he had them (wisdom does not equal good memory). And good ol' Shazam was always there to reinforce (perhaps with a touch of Laser-Guided Amnesia?) the idea that he had "only" the powers of Zeus, Mercury et al, defined as strength, speed, stamina, flight, invulnerability and wisdom.
 * Alternatively, He really only does have those powers, but Shazam was rather bored and decided to come up with random things his name could be an abbreviation for. Goddess knows I spent half of highschool Latin classes doing that.

Humans were alone in the universe on Earth-8
The White Entity from which all life is said to spring is both a post-crisis character, and said to originate on Earth, something patently impossible given that Oans (from Earth-1) predate Earth's formation. We also know that all post-crisis characters were originally from Earth-8. Obviously, Earth 8 only had humans, which explains the claim (he created all life in the universe in that world because all life in that universe was on Earth); because The Entity was discorporate when the universes melded, although his role as the Creator was expanded to the universe as a whole, his memories backstory of being on Earth at the time remained unaltered (we have seen characters in the afterlife to have had unaltered memories between the Crisises). Thus, what appears to be a timeline discrepancy is actually just Powergirl Memory Syndrome.
 * No.. it just... why does everyone assume that Earth-0 formed after Oa and the Fourth World. Nowadays it just seems like simple life developed on Earth, but advanced life developed earlier than that on Earth.
 * Of course, this raises the question of how to explain all the post-crisis characters that aren't from Earth.

Civilians come back from the dead almost as often as superheroes do on Earth-0
Their revivals are simply not documented in the comics, as they aren't part of interesting storylines.

Crisis on Infinite Earths didn't destroy all the alternate Earths, just separated Earth from the Marvel Multiverse by a long shot.
Marvel's Earth is called Earth-616, and DC and Marvel and a few crossovers. Not only that, the Almagam Universe is canon in Marvel. The last few Crisis crossovers in the DC universe have been about establishing that connection again, not recreating the multiverse.
 * It follows that the new 52 universes serve as a bridge to the wider multiverse, allowing for more than just the specified 52.
 * We on Earth-Prime are a part of this newly acessible larger multiverse. We were never destroyed at all- simply cut off from Earth-0 by a vast gulf of interdimensional space, which is why we had DC comics between the Crises, why we still have the suffix Prime rather than a number, why we're not among any of the described 52 universes, etc.

The Spectre's power level varies at God's whim
Which is why it varies such an incredible range. God either nerfs or twinks him out depending on the situation and how much of the situation He's willing to do semi-personally via His Spirit of Vengeance, and how much of the situation he wants His Creation to solve on its own, possibly via application of divine Power Limiters.
 * The fact that he was allowed to use so much of his power during the Crisis On Infinite Earths goes a long way to show just how dire the situation was
 * The fact that he wasn't depowered entirely before his Infinite Crisis rampage indicates that a human host is probably necessary for this divine power-limiting- maybe God is just telling the human how much leeway to give the Spectre, and the human soul holds him back accordingly?

Miss Martian is secretly Martian Manhunter in drag
Back in JLA #27, Bruce Wayne is meeting with Clark Kent in Japan, and Clark introduces him to a young Japanese woman named Hino Rei. Bruce immediately recognizes "her" as the Martian Manhunter. Apparently J'onn J'onzz likes to cosplay as Sailor Mars. Skip ahead some years later, where a new Martian character, Miss Martian, shows up out of nowhere to join the Teen Titans. Miss Martian likes to dress like a Sailor Senshi. Hmmm...
 * Miss Martian and Martian Manhunter have been seen together. Clearly, these were telepathic illusions.
 * According to The Other Wiki, J'onn J'onzz's notable aliases include Mrs. Klingman, Betty Nehring, and Joan Jones.
 * There was a JLA annual (#4) in which it's noted MM keeps multiple superhero identities around the globe. In particular, Batman suspected the Turkish superheroine Janissary to be J'onn J'onzz in disguise (she wasn't, though he was actually another Turkish superhero).

Mr. Mxyzptlk never really lost his powers during the Emperor Joker storyline
Mr. Mxyzptlk and Bat-Mite are shown as the most powerful beings in the universe. During the World's Funniest one-shot, they destroy multiple universes, including defeating the Specter a number of times as a running joke. Mr. Mxyzptlk gave Joker some of his powers just to get a good story because Mr. Mxyzptlk is bored (which, incidentally, is why he chases after Bat-Mite in World's Funniest). He didn't know whether Superman would defeat the Joker (because he didn't want spoilers), but even if Superman couldn't, Mr. Mxyzptlk would just put everything right again.

God in the DCU comes from the 5th dimension.
Mxyptlk is capable of deeds like easily overpowering the Spectre, despite the Spectre being the embodiment of God's wrath. The reason why he can do these things is because his power level is the same as God's. The truth is that God comes from the 5th dimension, and is the same species of Mxy. They may even know each other-God lets Mxy mess around because they're good friends.

Closely related, whenever you see the fifth-dimensional imp or Batman's biggest fan seem like they lose, it's just because it's more interesting for them that way.

Mephisto is behind the upcoming DC Universe reboot.
Undoing Spider-man's marriage was only a 'test run' on his grander plans for both the Marvel and DC Universes. His plan is to apparently revert the DC Universe to decrease the amount of superheroes and make it easier for him to take it over (covertly, of course). The other consequences (and that for the Marvel 'verse) are yet to be seen.

Post-Flashpoint continuity changes.

 * Green Arrow and Chloe Sullivan will become an Official Couple, like in Smallville.
 * Perdo, Eugene, and Darla will be imported into the main continuity as reimagined versions of the Lieutenant Marvels.

At least one of the Earth Born Angels will join Justice League Dark.

 * We haven't heard much from them since Kara Zor-El had been reintroduced into modern continuity.

The DC Universe is intent on integrating all other fictional universes.

 * Over the years it has folded various Golden Age heroes, Charleston, Captain Marvel all the way up to recent things like the Archie superheroes, Wildstorm, and Milestorm. The various Crisis events are the universe's way of digesting. Crossovers with Marvel like Amalgam and JLA/Avengers were attempts to absorb the Marvel Universe, but DC isn't strong enough yet.