Not adding any new ones, just clarifying the wrongs answers given.
Green Lantern. His weakness depends on which one we are talking about. Alan Scott (the first GL) 's ring was susceptible to wood. #2, 3 & 4, Hal, John, & Guy all shared the weakness of yellow built into the GL corps rings. Kyle Rayner's ring has no built in weakness. Ganthet removed it because it was the last GL ring at the time.
WonderWoman. She can be rendered helpless by tying her bracelets together, but only if they are tied together by a man.
Superman is only vulnerable to green and red kryptonite, and red technically doesnt' exist and he is vulnerable to magic.
The Flash (Wally) is unable to vibrate through matter on his own, a trick his uncle Barry mastered. Other than that, he has no weakness in his superpowers. His biggest weakness is being outsmarted.
Batman. Batman is a normal human and is vulnerable to a bullet in the head like the rest of us. He is usually just too smart to fall into any common criminal tricks. Batman's weakness is the unknown.
Spiderman's weakness is his sense of responsibility.
Add in personality flaws, (wolverine's temper, etc.) and that's about it.
Comic Geek Husband.