Frodo and the party at Weathertop - in the books Frodo shouts Elbereth's name as a war cry and stabs at a wraith, rather than cowering and falling down as in the film.

Ent moot results and dramatic reversal - in the books, the Ents knew what Saruman had been up to and decided to go to war at once. They didn't passively decide to do nothing then change their minds.

Faramir bringing Frodo and Sam (and the ring to Osgilath). In the books, Faramir recognized the threat the ring posed and let Sam, Frodo and Gollum go on with their quest without hinderance.

The books had no nonsensical scene with Gollum framing Sam for illicit lembas consumption.

The books had no stupid dwarf tossing jokes.

While Aragorn has periods of self doubt in the books, none of these inhibited him from taking action. In the film he has a long sequence of scenes where he's basically paralyzed by self doubt.

No scourging of the Shire in the films. These scenes were crucial to showing just how much each of the hobbits had developed as characters and in what ways.

I could go on, but hopefully these are sufficient to illustrate the point.

The films were great with respect to casting, cinematography, art design and location. Jackson and Boyens seemed to have forgotten however that Tolkien was the master and they the students with respect to writing.