First, I'm not sure what you mean by "Changes that you weren't bothered by". There are changes that I feel indifferent to, changes that I'm not too happy with, but willing to accept, and changes that I actually like.
Good Changes
-Bombadil, I really don't mind. In fact, I'm glad they cut him. I don't think he'd look good on screen. (Imagine...all the Nazgul encounters set this dark and creepy atmosphere. Then all of a sudden, there's this guy who laughs at everything, sings at everything, and handles the Ring like a piece of stone. Not only does he bewilder the audience, it sort of takes away from the beginning atmosphere...which is usually the most important.
-I'm glad they actually showed the scenes instead of them talking about it, but I don't see how any sane movie director would have done otherwise
Changes I feel indifferent to
-Warg attack was nice...don't really see anything wrong about it.
-Eomer being reduced to an extra.
(Wasn't too fond of him anyway
)
-Imrahil and Beregond being cut.
Changes I dislike, but willing to accept
-Showing Arwen was a nice touch, since they had to make the people realise who this Elf that married Aragorn was, but I think they overdid it. Especially in RotK with her "dying" and seeing her future son.
-Scouring of the Shire cut. The main complaint I hear about LotR is that it's a too-happy ending (unlike the book's bittersweet ending). I think this may have changed that opinion. But I suppose the movie's got to end somewhere.
I do have a whole lot of changes that I WAS bothered by, but these are the MAIN ones:
-All the magic mumbo-jumbo
Theoden being exorcised by Gandalf, Saruman's fireball (RotK EE), Wizard duel...I suppose I should be glad that Gandalf didn't kill orcs with lightning.
-The Demented Father and Wicked Sons
Faramir becomes evil. Denethor is a madman who hallucinates (RotK EE). 'nuff said.
-The Dead at Pelennor....?
Seriously, why didn't they follow Tolkien in this? It could've been done much much much better. Grey mists, echoes of a battle, eerie voice out of the air, terrifying the enemy instead of rolling into them...I think this part had the potential to be one of the best scenes ever out of all 3 movies.
I also think they cut
the most dramatic scene from the book. Gandalf facing the Witch King at the Gates of Minas Tirith. This was the scene that moved me the most from the books, and I'm disappointed this got completely cut in the TE, and tampered heavily with in the EE.