The Hobbit's Age- Didn't bother me at all, surprisingly enough.
Wargs- Though they are a far cry from the books description of the wargs (IMO), the new version of them didn't bother me very much.
Elves at Helm's Deep- One of the bigger changes and yet it is on this list, strange. But it seemed to fit well with the story (although I didn't think the Galadriel/Elrond telepathy scene before that fit nearly as well) & I could find no problems with it that I lost sleep over.
Wizard Fight- Though I wouldn't say it's one of my favorite parts, I justify it on much the same grounds as the elves at Helm's Deep--it fit well & wasn't horribly wrong. Now if they would've brought the fireballs, force-lightening, and bursts of magic sparks into the action...it'd be a much different story.
Eomer taking over for Erkenbrand- Pretty much the same thoughts as
Boromir88's. They needed to leave out more than just a few characters & Erkenbrand had crosshairs on him (though it would've been cool to see Eomer fight in Helm's Deep

).
I'm sure I'll post more from RotK once I watch the extended version tomorrow night.