Absolutely love the films, they are an almost perfect adaptation. Still I would liked to have seen Tom Bombadil in the film and the scouring of the shire where Saruman really dies, still his death was very good. And these omissions never really upset anything,
One change from the books that really worked for me was when the Elves turn up at Helm's Deep and fight to defend it, it's a powerful moment when they first appear. Haldir dying was really sad and moving, he looked so pure amongst all the carnage.
The extended versions are the only way to see these films imo. The wonder of cinema at it's best. And the best extras I have ever seen.
All in all they are a master piece.