I got the platinum mumble extreme edition of the Two Towers and listened to the director's commentary during the parts where the plot diverged radically from the book. A recurring phrase they'd use was "a slight deviation".
Yes, and the way they used it made it sound more and more like a running joke among the scriptwriters, a bit like a film-maker's version of "just a quick pint". By the end of the commentary they were actually sounding pretty apologetic for the deviations ("the choices we made early in the filming meant that...").

It did make me laugh, in the first film, when the scriptwriters poked fun at Tolkien's long pieces-to-camera with the backstory: when Aragorn is singing the Lay of Leithan, and Sam asks him what happened to her, and he says "She died". In the book his answer to that question goes on for a page and a half.

Peter Jackson has essentially said all along that he ran The Lord Of The Rings as two projects in parallel: a film of the book, in the extended editions, plus a film of a palimpsest of the book, in the cinema editions. I think he's done that extremely well so far. He also says in one of the commentaries, that even where they've monkeyed with the plot, they've always striven to keep the visuals "authentic" -- from the two-trees-based decor of Rivendell to the flowers on the tombs of Edoras -- so that readers of the book always feel "at home" there. Basically I've got a huge amount of respect for the whole undertaking, and I cannot but imagine that the third film will live up to the first two.

Peter