Frodo sending Sam away on the steps of Cirith Ungol

Turning the Ents from wise and venerable creatures into comical half-wits

Having Faramir submit (temporarily) to the temptation of the Ring and take the hobbits to Osgiliath

Cutting "The Scouring of the Shire"

Incorporating a significant amount of material with Arwyn, originally in the appendixes, into the main story as a tacked-on romantic sub-plot.

Making Sam so much less awesome

(Not that movie Sam isn't cool, but many of the character's defining moments have been cut or downplayed. Notably:

• "The Choices of Master Samwise"
• his song in the tower of Cirith Ungol
• his epiphany with the star
• his final confrontation with Gollum on the slopes of Mount Doom)