I haven't actually finished Return of the King since sixth grade, I've tried a couple of times got through books 1-4 and then 5 ruins it for me, so this might be a little iffy.
I liked how Peter Jackson did the Bilbo's house and that it's nice to know that it was kept in storage after production. However I wish that Frodo had sold it to the Shakville Bagginses (probably butchered the spelling there sorry.) making it harder to come back to after the war is over.
I am not really sure what I liked in the movies that wasn't in the books. I guess Pippen and Merry's drinking song while they're still in Hobbiton, I'm not sure if it's in the theatrical version though since I own the extened editions.
I wished they had explained that there was more than just two wizards in all of Middle Earth. Tom Bombadil is an amazing character, and is reflected wholly in the Black Label game for Fellowship. And the scouring of the Shire should have been in Return of the King, even though it was in Fellowship it would have pointed out that even the Shire had been corrupted.
I don't remember how I saw them in my mind, but I think I saw Eowyn differently, and Legolas really seemed like a background character that I never paid attention to. But I did like Strider as he was in the book and Aragron's background story helped with that. I didn't see him as foreboding as he first appeared in the movie.
Bombadil has to be my favorite, but I was always wanting to read about the hobbits, because that's where the excitement was, I didn't want to read book five, but I could have missed something.
"Ai, Ai, a Bolrog." has to be my favorite part in the book, and Merry and Pippen's drinking song in fellowship has to be the best there.