RE; the lord of the rings trilogy.
First off, I did enjoy them, especially the extended versions,however.
As you previously stated, they left out Tom Bombadil (understandable, but still sad)
which required them leaving out the barrow wights,and how the sword pippin uses injures the witch king of angmar;
also screws up old man willow pretty good vs the book.
I understood, but regret the removal/merging of Glorfindal and Arwen.
The whole fuck up about Faramir taking frodo, instead of re the book, realizing how important what he(Frodo) is doing is vs his (Faramirs) desire to please his father, again weakining Faramirs 'Charactor' Vs Boromirs 'Charactor'
The MAJOR (IMO) leaving out the Scouring of the shire, which is the whole point of the entire quest, showing how these four hobbits have matured into truly great people, vs how self centered and selfish they were at the beginning. (also gives meaning to the whole farmer maggots crops section)
the murder of saruman on Orthanc instead of in the shire,
the 'enlightenment' frodo has acheived by the end of the story whereas he doesn't condone any killing, no matter how justified.
Those are off the top of my head, but as I said I did enjoy the films no matter how badly they mangled parts of the story.