This article is from the X-Men Comic Books FAQ, by Kate the Short (firstname.lastname@example.org) with numerous contributions by others.
It's hard to tell, exactly. Mutation in the Marvel Universe often
occurs during extreme physical or psychological stress. Combining the
removal of everyone's powers by High Evolutionary with increased sunspot
activity (radiation) has apparently created a bumper crop of odd power
increases and mutant births all over the world.
That said, there are a few obvious cases of this "secondary mutation,"
as well as a few other characters who have shifted appearances:
* Angel: Not a secondary mutation, apparently. His shift from metal
wings to feather wings is apparently due to Apocalypse's mucking
with his DNA and that eventually wearing off. He lost his blue
skin pigment in Uncanny X-Men #411 after Black Tom Cassidy drained
his life force.
* Beast: Secondary mutation. Evolved into a lion-like form. Gained
strength and speed.
* Emma Frost: Secondary mutation. Gained an extremely tough diamond
exoskeleton which can block physical damage and radiation. However,
she can't use her telepathy in this form.
* Iceman: Secondary mutation? After the events of the X-Men Forever
miniseries, gained the ability to become "living ice," and seems
to have his flesh turning into ice on a permanent basis.