Top 5...

[Eomer of the Rohirrim]

1. Wargs were replaced with suicidal hyenas.

2. No Warg scene on the way to Caradhras (or was it Moria?) where they surround the fellowship, Gandalf kills a few, etc.

3. Ents, especially Treebeard, treated as boring and stupid.

4. Frodo/Sam/Gollum lembas saga

5. Giant flaming eyeball (can't believe no-one mentioned this yet).

[Lalaith]

1. Major characters given personalities diametrically opposite to how Tolkien created them...eg Tolkien-Theoden "kindly old man" while film-Theoden angry and bitter, in fact playing the role of book-Denethor;
meanwhile Denethor himself - a leader who in the book did his utmost to defend Gondor, ordering the beacons to be lit and the Arrow to summon Rohan: "tall, valiant, more kingly than any man that had appeared in Gondor for many lives of men") turned into a drooling Nero-esque sybarite.

2. Major characters who were not actually transformed were trivialised and made oafish (Gimli, Merry, Pippin) or embarrassingly wet and over-emotional. (Frodo, Eowyn)

3. The stupid Arwen-into-horse scene in TT (didn't actually mind the Arwen-on-horse in FotR)

4. The stupid Treebeard-tricking in TT

5. The stupid Arwen-is-leaving-then-dying thing in TT

1. Ents, especially Treebeard
2. Frodo/Sam/Gollum lembas saga
3. The stupid Arwen-into-horse scene in TT
4. Giant flaming eyeball
5. Elves at Helm's Deep

[skip spence]

Off the top of my head

5) Turning the horror-scenes of the book into action scenes (ie. Black Riders, The Balrog...)
4) The stupid action scenes, like Legolas' ridiculous shield surfing, his climbing of ridiculously big Olliphants, the Dwarf-tossing, Sam fighting with cooking ware etc...
3) Denethor the retard
2) Stupid Ents (they actually annoy me in the books too, maybe I should start a thread about pet peeves in the books too?)
1) Almost about the entire RotK. In fact, don't think I've ever managed to sit it through.