Other than the core basics of Seigel & Shuster's origin...
The idea that Kryptonians gain their powers from Earth's yellow sun and atmosphere. I think this is a wonderful addition to origin that was introduced during the Weisinger era, I believe.
I like Byrne's idea of Clark's powers developing slowly, rather than having them all right away. I also prefer Lana being in on the secret while Pete isn't.
I like Johns's explanation for why Clark starts wearing glasses so young. It's very Cyclops, but a good idea is a good idea.
While I'm not a fan of Superboy being a publicly known hero in Smallville, I think the idea of him having adventures in the far future with the Legion of Super-Heroes is a great one to explain how he became so proficient in his superpowers.
I'm a fan of the Pa dies of a heart attack while Ma lives version of him leaving Smallville. I think it's a great way of illustrating his journey from boy to man by giving him the most painful reminder of the limits of his amazing powers. The Donner film nails this perfectly.
Once we're in Metropolis, I think Lois being the one who names him Superman is essential. Not sure where this idea came from though.
Other than that, I think there's a lot of different flavors and interpretations of the origin I enjoy, but those are the strongest elements to me.
I like the idea that Smallville had of Kryptonite being brought by Clark's spaceship. Explains why they're so common on Earth.
I know it's controversial, but i actually liked the Byrne bit about the birthing matrix. Combined with the snow storm it removed any of the orphanage and adoption problems from the Silver Age origins. Now it was just taken for granted that Clark was the Kents' natural kid rather than giving one more clue to the dual ID (unrevealed parents).
Morrison's adding the more rough-and-tumble Action Comics #1 Superman as a stage in Clark's development. Superman starting out as a less law-abiding vigilante and developing into a more civic minded hero works for both meta and story telling reasons.
The original take of Clark not knowing from day one about Krypton being restored in most post-Crisis origins. His discovery of his true nature whether around puberty (Secret Origin, Man of Steel film, Smallville) or as an adult (Man of Steel 1986 comics' mini-series, Lois and Clark TV show) provides better character moments than the Pre-Crisis where he knew every detail from infancy (or via memory chair as a young Superboy).
- the birthing matrix allowed to have it both ways: makes him immediately more alien to us than a naturally born child who's been shuttled, but also with the idea of the snowstorm it allows him to pass as a naturally born child.
- the relatively young Kents seen in Birthright or New 52
- Clark grows up in Smallville as seen in Secret Origins '86 or Strength
- travels the world as seen in Birthright and Zero Hour, comes back to the US as seen in World of Metropolis, but begins in Metropolis more like we saw in Man and Superman
- learns of his origins in a random way, like he did in the Golden age
- has mind wiped Legion adventures like Johns did
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