Dr. Miles Hawkins from M.A.N.T.I.S.
John Locke from Lost
(paraplegic before the Island heals him).
Gary Bell (autism), Erin Way (can't retain long term memories) and Anna Levy (severe apraxia
of speech and body movement) from Alphas
. Initially, all the characters had frequently severe negative side effects to their enhanced abilities, but that's been less of a problem for some as the show has gone on and their skills have advanced.
Jason Stryker/Mastermind(sort of) in X2
who is confined to a wheelchair and mute after a lobotomy.
A bunch of veterans in Starship Troopers
who were missing limbs (that were replaced by cybernetic ones) or had other combat-related ailments, including Lt. Rasczak, the recruiter, and the blind teacher played by Rue McLanahan.
Elijah Price (Mr. Glass) from Unbreakable
(Osteogenesis imperfecta or Brittle Bone Disease).
Steve Austin and Jamie Summers --The Six Million Dollar Man
and Bionic Woman
respectively-- both lost limbs and an eye and ear respectively in accidents before having them replaced by cybernetic implants.