I can think of a few.
Phoenix, Cable (or the clone Strife), Franklin Richards, Iceman, to name a few.
http://en.wikipedia.org/wiki/Mutant_(Marvel_Comics)#Omega-level_mutants
See the problem I had was this:
Are they really heroes..?
Phoenix = killed a planet
Cable = turned all the people in the world pink... (even though it was just temporary..)
Franklin Richards = he's a kid...
Iceman = sure, he's a good guy... but his immaturity... is he really up there with Cap Am and Thor..?
But to prove I'm not mutophobic:
Marve mutant theme:
Cyclops Beast Wolverine Professor X Magneto Scarlet witch En Sabah Nur PHOENIX
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