All-Star Superman/WMG

Jimmy Olsen knows Clark is Superman.
Jimmy gives Clark a slightly suspicious look after Lombard’s toupee caught fire and stammers slightly before referring to him as Superman after he had “disguised” himself as Clark Kent.
 * Morrison said in a 2008 Newsarama interview that he believes Jimmy already figured it out, but believes Superman has fucking heat vision a good reason for keeping his identity secret so Jimmy plays along.

Leo Quintum is Lex Luthor.
(This theory originally by Cole Moore Odell) Leo Quintum from All Star Superman is an incredibly rich scientific genius with grandiose plans for the future, young attractive female assistants, and a collection of anti-Superman weapons. He's clearly presented as Luthor's benevolent counterpart, but maybe there's more to it. Superman's only failure in the series is his inability to reform Luthor. But maybe he actually does. Luthor sees the error of his ways, travels back in time, gets some hair plugs, and assumes the Quintum identity. Not as part of some evil scheme, but in a genuine attempt at redemption. Superman recognises him instantly, but also trusts that he's actually reformed. Now Luthor's only flaw is making too-clever-by-half references to the scheme when talking to Superman: Quintum's coat and goggles being so similar to what Lex wore on his rampage is just more evidence. As is what the general says, when Lex is ranting at Quintum in the first issue:
 * "I could be the devil himself for all you know."
 * "I'm trying to escape from a doomed world too, Superman... it's called the past."
 * "Talking to yourself again, Lex?"
 * Lex Luthor also has a pet monkey named Leopold.
 * Holy crap, this makes perfect sense.


 * A bigger clue occurs in the symbolic imagery, which Morrison loves. In Ish #1, Leo tells us that 'I stole fire from the Gods', representing the classic creator of humanity, Prometheus. Prometheus' brother was Epimetheus, whose wife - Pandora - opened up the box that created evil in the world.


 * Now, Epimetheus' name translates as 'Hindsight', and Prometheus' as 'Foresight'; Prom had the foresight to create humanity as Earth's ideal lifeform, and lock all the evils in a box, while Epim only had the hindsight to think of keeping that box out of the hands of his wife. If we can glean from Leo's statement that he is symbolically Prometheus, and presume that he is also Luthor, then Luthor becomes Epimetheus - where the one has the foresight to know that Superman will die, the other only becomes a good man through hindsight. QED.


 * Frank Quitely's art gives us some clues in Issue 1 - Leo's eyes are obscured in two panels: "I...don't know how to tell you this, Superman', and 'Luthor has used us to kill you.' Implying that he's hiding something when he's talking.


 * Aditionally, there is a close-up shot of Luthor saying 'Before I do something REALLY terrible to Superman' that mirrors the earlier shot of Leo explaining exactly WHAT that terrible thing was. You can see that the biggest difference are the specs, the hair and the slightly pointier nose.


 * "Quint" denotes the number five. Lex Luthor's inmate number is shown to be 221. 2, 2 and 1 have a sum of 5(a "Quint-sum", if you wanna stretch). Associating a set of numbers - or any symbol, label or name - with a character is not the kind of opportunity Grant Morrison tends overlook.


 * In Issue 8, Leo tells Lois the bad news about Superman dying, and about his possible death in the Underverse. In the former, he phrases his language specifically so that he would HAVE to tell her; and in the latter, you can see a dark look over his eyes, and a suppressed grin, almost as if his original persona is peeping through.


 * In Issue 10, both Luthor and Quintum appear before Superman under glass; Luthor behind the prison barrier, and Quintum behind first the bottle of Kandor and the helm of his astronaut suit. The astronaut suit is more important, because unlike the prison barrier, it's a glass that he's made, and one from which he's humble and thoughtful rather than arrogant and angry.


 * In Issue 12, Superman's last words to Luthor are "You could have saved the world YEARS ago if your tried, Lex". Leo's dialogue later includes the line, "A world without Superman...THERE'S a challenge to human ingenuity". Superman has challenged him to be better, having seen how good he COULD be through Superman's eyes. That's also why Superman gave him the super-powers formula; knowing that Leo is Lex, he knew not only that Leo had already known what it was like to take the formula, but had also not attempted to make some more of it since returning to the present.


 * This theory is possibly Jossed by Morrison himself. In an interview with Newsarama, he gives a lot of background info on Quintum, explaining some of odder things Quintum does in the series (including the "devil" comment mentioned above), but he never even hints that Quintum might be Luthor. Essentially, Quintum is supposed to be the good scientist, a counterpart to all the evil scientists (including Luthor) we've seen in superhero comics. So he's linked with Luthor on a thematic level, which would explain the juxtapositions in the comic that prompted this WMG. But he isn't Luthor.
 * It's not canon, but the animated movie version of All-Star Superman also disproves this theory. The movie versions of Quintum and Luthor are clearly two different people, voiced by different actors. Interestingly though, in the movie the good scientist/evil scientist dichotomy of Luthor/Quintum Unlike in the comic,
 * It's not really so much jossed, so much as Quintum is supposed to be there to get rid of the Science Is Bad aesop that pervades so much of the DC comics universe. According to Morrison, Quintum is a trickster whose background is deliberately vague (he calls him "The Man who Fell to Earth"). While he is obviously the good counterpart to Luthor, any further connection between them is up to the reader - but subconsciously or not, there is a lot of implications going on in the comic (and even the animated adaptation can be resolved - how many stories have you read in which a time traveler imparts information to another version of himself) that hint that they may be the same person. I think what went on was that this is one of those subconscious implications on the part of the writer. Morrison said that he didn't realize it directly, but that Quintum was obviously based on Willy Wonka. Similarly, the intention might not be there, but the text supports the theory that Quintum and Luthor are at least closely related in some way since the character's formula essentially seems to be: Good Guy + Lex Luthor + Willy Wonka.
 * I've read many stories where "a time traveler imparts information to another version of himself", but it's always the future version that gives the information to the past version. But in the animated movie, it's Lex (the supposed past version) who gives the information to Quintum (the supposed future version). And after that, when Quintum is alone, he seems genuinely surprised by Lex's discovery. Which would maker little sense if Quintum was a future version of Lex.
 * It could also be Morrison refusing to breach that brilliant, deceptive, Clark-Kenting-made-real aspect of his story by just giving it away. The fact that a character as monumental as Quintum gets zero backstory in either the story nor the 9-part interview is suspicious, to put it lightly.
 * The reason he has no backstory is explicitly explained by Morrison in the interview linked to above.
 * There's also the fact that Quintum has a thin body type (he describes himself as an ectomorph), whereas Luthor is much more bulky and muscular. Of course it's possible Luthor somehow changed his body type to disguise himself better, but that's kinda stretching it (no pun intended).
 * It says in the last few pages that after Luthor had his Heel Realization and Superman flew into the sun, he "diminished". Could be that a few months of not working out quite so much his body became trim rather than muscular. Having lost his jealous hatred for Superman, he no longer feels the need to look like him. He also finally got around to curing his own baldness, and dyed his hair blonde so he wouldn't look like just a skinnier Lex Luthor with hair. The glasses and colorful coat help with his disguise.
 * As for the movie, there's no reason that it isn't just an alternate continuity. McDuffie might not have known Leo Quintum was implied to be Luthor, and so he changed the ending from Kal-El giving the Superman 2 formula to Quintum to Luthor doing it. It could just because in that version Luthor is NOT Leo Quintum. Who knows?
 * Considering that McDuffie and Morrison are both long-time DC writers, and that Morrison is one of the biggest names working for DC at the moment, and that the movie was very faithful to the comic, it would seem rather unlikely that McDuffie wouldn't have consulted Morrison while writing the script, or at least sent the script to him for his approval. So yeah, it might be an alternative continuity, but if Morrison meant Quintum to be Luthor, I'm sure McDuffie would have known about it. In my opinion the movie actually gives Luthor a better ending than the comic, because now we get to see his Heel Face Turn instead of theorizing there might've been one, based on a few esoteric clues. Being oblique is not necessarily the best way to tell this story.

Leo Quintum is Luthor's clone sent from the future to help Superman and live up to his promises of Altruism.
Because that would be awesome and very Morrisonish.

Leo Quintum is the result of one of Luthor's experiments.
When Lex/Leo was first getting into the mad science business, he accidentally split his good and evil sides into two people.

Lex knows that Clark is Superman, and orchestrated the entire prison interview....
.... as well as his subterranean cave with chauffeured rowboat exit JUST FOR THE PLEASURE OF CREATING AND GETTING TO WATCH the visual metaphor of Superman being boated across the river of the dead into the underworld. Even though this troper prefers to think Luthor's ego is so big he's pretty much incapable of realizing Superman is Clark even when it's literally staring him in the face, the idea of Lex pulling a scheme like this is almost as cool and in-character. It also offers an alternative explanation for Lex's lack of shocked revelation when a finally glassesless Clark is shouting in his face from six inches away.
 * Jimmy Olsen hasn't known Superman as long as Luthor has, and Jimmy also isn't the smartest man alive. If Jimmy Olsen can figure out Clark is Superman, Luthor can, though I appreciate you outlining it.

Leo Quintum is basically Brainiac 5 of the Luthor family.
Brainiac is a Superman villain like Lex, bald and super-smart, except green-skinned and an alien. He has a descendant in the 30th Century named Brainiac 5, time-travelling, blond-haired and super-smart, who uses his powers for good to make up for his ancestor's evil ways. Leo Quintum, (Quintum=5)is also blond-haired, super-smart and his remarks about trying to escape the past can be seen as trying to escape his family's history of evil. Leo Quintum = Good Lex 5.

Leo Quintum is one of Jack Kirby's Hairies.
The Hairies were youthful, genetically-engineered super-geniuses from the DNA Project Jack introduced in his run on Superman's Pal, Jimmy Olsen. After the rest of them had moved on to other things, Quintum took the reins of his alma mater, renamed it P.R.O.J.E.C.T., and continued developing all manner of over-the-top Kirbyesque technology, like missions to the sun and giant human clones designed to explore Saturn.