The only thing that Jackson changed that really got under my skin was the Elves showing up to Helm's Deep. Helm's Deep was supposed to represent humans being able to defend themselves without the help of the other races. By having the Elves showing up to save them it completely destroys this point.
That and Gimli being changed into comic relief was a bit annoying.
Almost every other change in the movie was understandable and didn't really bother me too much.