To me, the most critical questions for a supers setting are the relative power level of the supers, the opposition, and general motivations of the characters. In that light, some random thoughts on your various suggestions:
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- The supers are the result of a large scale extradimensional accident.
This would be pretty cool if all the supers were normal folks in a setting somewhere between WWII and near future. For whatever reason, extradimensional rifts are popping up everywhere and letting things from beyond through. An entity of some sort grants the PCs the powers and charges them to do a job or they just get them by accident and have a natural instinct to close the rifts.
The game is bouncing around, high action, as the PCs (alone or in groups) try to keep the world from falling apart at the seams. I like this because the opposition can be varied, but almost always non-human. The PCs have a strong motivation in general. Also, the power level can vary dramatically just based on how you design the foes.
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- The supers are abductees returned to Earth.
This can go a few ways. If the PCs were abducted before an apocalypse and returned after, you could get interesting stories as the PCs try to regain some of the lost glory of earth and bring together some of the survivors. Opposition would end up being the elements, horrible mutants, and the environment itself. I'd be mildly interested, but post-apoc always seems to focus on man's inhumanity to man more than I like.
In a more modern day setting, the opposition either ends up being other abductees or the government, neither of which really thrill me. The same goes for futuristic and WWII. Alien world could be interesting, but would likely end up kind of dark if the PCs didn't have a clear way to get home eventually.
You could bend the idea a bit and have the PCs not be the abductees themselves, but their descendants. The original abductees pushed forward human development to the stars and now the descendants are leading the charge. Elements of Aberrant seem to creep into that idea in my head.
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- The supers have always existed in secret, and are the result of demigod bloodlines.
I don't have good ideas for this one. Modern-day, it's pretty much Scion. On an alien planet might be interesting, but you'd have to have a good reason for a bunch of them to have been on the same ship.
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- The supers are the result of a brilliant but deranged scientist, nazi-style.
You can get some of the before/after thing with a post-apoc here, too. WWII seems the most natural, but is kind of just Captain America.
An interesting way to do this would be to combine it with the first idea. The PCs are modern day people that get abducted by a UFO that takes them into the center of the hollow earth where Hitler has survived with his super-nazis. The PCs get experimented on, something goes wrong, and they escape. That'd be kind of cool.