Just figured I'd mention that Superman is also vulnerable to magic, and he doesn't do too well against psionic powers. He also has to breathe, even though he can go a loooooong time without it, but it seems that with enough yellow sunlight around him he can forgo breathing, but it has to be a lot. Radiation from a red sun will drain him of his superpowers instantly (but was that just Pre-Crisis?), and if removed from sunlight, he will slowly lose his powers.
Hey, let's list some more...
Wolverine - anything that negates his healing powers will kill him, as his metal bones would kill him without his healing powers. Magnetic powers are also very effective against him.
Venom, Carnage - fire and sonics
Storm - claustrophobia
Green Lantern - the color yellow...
Professor X - stairs (sorry! sorry!)
Magneto - plastic weapons, nerf bats
Thanos - his own ego
Galactus - plain old hunger
Apocalypse - he keeps burning out host bodies apparently, so I guess you could say old age. He does not have a weak point in the back of his neck. That's from the old cartoon show, and even on the show the weak point didn't work.
Mr. Sinister - Cyclops's optic blasts
But yeah, pretty much all heroes/villains have weaknesses. I wouldn't confuse a weakness with a limit, however.
EDIT: Wait, Spiderman does have a power weakness: Venom. Venom negates his spider sense. Almost forgot about that. And to be fair, Megneto has shown the ability to manipulate both forms of energy other then magnetism and non-ferrous materials before (on rare occasions), but Marvel has quietly forgotten this. And for the record, I think Grant Morrison was one of the best things to happen to the X-Men, but that's another discussion.