5) Luke Cage - Adamantium
Luke Cage has skin that's as strong as titanium. So the only thing that can puncture it is a fictional, indestructible metal that is stronger than any other metal. Pretty straightforward. Kinda boring, but it makes sense, at least.
4) The Flash - Running Too Fast
Barry Allen is a fast dude. So fast, in fact, that he can pretty much just jump around in the time stream however he wants (though he isn't too good at changing events to his benefit). He's so fast, in fact, that one time, during the Crisis on Infinite Earths, he ran so fast that it killed him by pulling him "permanently" into the Speed Force, the energy field that gives speedsters their power (he came back, because, you know, comics). It just seems appropriate somehow that a hero's very own power is the same thing that kills him. Especially when it's speed.
3) Daredevil - Noise Pollution
Daredevil sees with his ears. So it only makes sense that the thing that would incapacitate him is the auditory equivalent of wool over the eyes. But instead of wool it's white noise or a bunch of babies crying or being right next to a huge ringing bell. Or, I guess for a really creative villain, just some super glue and a nice thick set of earmuffs.
2) Adam Strange - Earth Withdrawal
If Adam Strange stays on Rann - the planet he goes to so he can have superhuman strength, go on awesome space adventures and hang out with his hot space-babe wife - for more than a year, he dies. Yeah, it sounds kinda arbitrary and weird that he would have to leave Rann once a year to avoid dying. But as far as story is concerned, it's beautiful. It keeps Adam Strange from ever getting too far away from his humanity. No matter how much time he spends on Rann, he'll never be a native. It keeps Adam Strange's story going, which is just what a weakness should do.
1) Superman - Kryptonite
People love to rag on kryptonite. They say it's stupid that Superman is vulnerable to stuff that his own planet was made of (but see, the problem with that is that it's the stuff that's the result of the planet being destroyed, kind of like nuclear waste). They think the different color variations of it, like the red kryptonite that has a different effect on Superman each time he comes in contact with it, are silly. They think it's dumb that something so rare could pop up so often and just happen to fall into the hands of Superman's villains. (Okay, maybe I'll give that one to them.) But like it or not, kryptonite is the quintessential superhero weakness. It is the weakness upon which all other weaknesses are built. It has become a synonym for weakness
. Just ain't no denying it, folks. No matter how many terrible songs Three Doors Down makes about it, kryptonite will be number one.