I will preface this with the usual disclaimer. The Lord of the Rings is hands-down my favorite book in the world. So naturally I'm a bit, erm, conservative about any adaptation. However, I don't think I'm blind to the necessity in some cases. I thought The Two Towers was magnificently done, even though much was changed. And if you look closely in the comments below, there will be quite a few cases where I say "this wasn't like the book, but it was good". So there.
Anyway. Some points, in no particular order:
The opening story of Smeagol getting the Ring. Parts were good, parts were awful. The beginning with him and Deagol on the boat was too slapstick, like something out of Dumb and Dumber, not at all fitting to the tone of the story. The fight was good, as was his transformation into Gollum; though I think the closeup of him eating the raw fish was just a little too gross for the tone of the film. A cutaway just before he bit, with some slavering sound effects, would have been just as horrific without being disgusting.
They took out the fact that Denethor had a palantir, which removed a lot of the reason and motivation from his character (the fact that Sauron had been warping his view of the world, driving him to the levels of despair that made him kill himself and try to kill Faramir. They even obliquely referred to it, as Denethor told Gandalf "I know more than you think I know. I know who travels with you...." ...thanks to the unmentioned palantir! It wouldn't have taken much, it was all of three lines in the book....
I liked what they did with the Paths of the Dead; that was the one part of the book I always had trouble visualizing. But why, oh, why, did he make them have to beg to be released at the end? Aragorn is too honorable to pull that shit.
Elrond visiting Aragorn at Dunharrow. In the book, it was Elrond's sons and a contingent of elves who came with a message from Arwen (who, by the way, was *not* dying - I don't know where that came from). On the one hand, the way that Elrond convinced Aragorn to go by the Paths of the Dead, and gave him Anduril, was decently done. But him being there at all was just ridiculous, Kirk-and-Spock-transporting-to-the-enemy-p
Having Pippin light Gondor's beacons to call for Rohan's aid. In the book, the beacons were lit as Pippin and Gandalf rode to Gondor. Having Pippin light them by subterfuge against Denethor's will was an interesting touch, ostensibly bringing more direct action into the story, but also implausible, as the first thing the guards would have done would be to douse the fire before the next beacon was lit. And while the dramatic visual sequence following the beacons' lighting along the White Mountains was beautiful, it also triggered my WTF?! button. Beacons at the very peaks of mountains, above the clouds, where getting the wood up there, let alone men to watch and light them, would be next to impossible... say what? Not to mention that the sequence of beacons they showed would have had them traveling halfway across Middle-Earth, not just the mere couple hundred miles from Minas Tirith to Edoras.
Gollum driving the wedge between Frodo and Sam on the approach to Cirith Ungol. There was none of this in the book; but it was well done, I have to say, and very true to Gollum's character. The only part of it that didn't ring true was Sam leaving. He would have followed as long as he could, and then I think sat down and died of grief before he turned and went back.
Shelob was excellently done. Though I am sad that they took out the orcs noticing that she'd been wounded, and them making Sam out to be a great elven warrior. That was a beautifully humourous, human touch from the original, which as with so many others were taken out.
As Faramir and company return to Osgiliath, Pippin sings Denethor a song of the Shire. This part is one of the most beautiful pieces of direction I've seen in a very long time. Hats off to Mr. Jackson for that one (and of course, lordandrei was in the restroom and missed it!).
When Eowyn picks up Merry before the ride to Gondor. Dramatic, but I thought they ruined it. Neither Merry nor the readers are told that the rider who carries him there is Eowyn until the battle with the Nazgul, which made for the battle itself carrying more of an impact.
The battle between Eowyn and the Nazgul. Very nicely done, though I wish they'd kept closer to the actual dialogue.
Gandalf summoning the eagles at the final battle: beautiful, and a wonderful link back to him escaping Orthanc in Fellowship.
The crowning of Aragorn. Aaaaaaaaarrrrggghh, this was all wrong. Frodo was supposed to be holding the crown, what the hell was Gimli doing up there? And having Arwen show up as a surprise, give me a break. And the worst of all, having Aragorn just sweep her into the cliched embrace in front of everyone. It was bad enough in the previous films having him mack all over her in the seclusion of Rivendell. It would have had so much more power, and been true to the majesty of the original, for him to simply take her hand, hold it a moment, and then lead her up the stairs.
I am okay with them skipping the Scouring of the Shire. Even in the book, it was an anticlimax, and the movie just didn't need it. As with Tom Bombadil, it would have been nice to see... but I understand why it got cut.
Mumakil (elephants) in the battle for Minas Tirith! Okay, this was cool, I have to admit. Initially Faramir and company slaughtered the Mumakil just before they encountered Frodo and Sam, and they never made it to Gondor. Since they cut that, it was cool to see them on the screen, though it did mean Sam still never got to see an oliphaunt.... (see above mention of human touches from the book that were stripped)
The fight scenes were just too much. You were numbed to them before the walls of Minas Tirith were even breached. If the direct view of the initial overrun of Osgiliath had been cut (which confused me anyway since we saw it in The Two Towers - was this the same battle, or a different one?), and the Minas Tirith battle shortened by 60% or more. Then the fight in front of the Black Gate would have had more of a feeling of that desperate last stand. As it was there was desperate last stand after desperate last stand, long past when there was any point in really caring.
Oh, and a nitpick about the walls of Minas Tirith while I'm on the topic. One rock and an entire tower comes down??!? Come on! That's like stormtroopers collapsing unconscious after a single right hook. If the city were that easy to destroy, they wouldn't have needed ten thousand orcs.
I was dismayed to see them take out Beregond, the guard at Minas Tirith who takes Pippin under his wing. Granted, this story would have taken valuable screen time, but it added so much to the human element of the siege of Gondor. In The Two Towers they stuck in this new story of the woman and her children of Rohan who were separated at the beginning and reunited at Helm's Deep, which I thought did a wonderful job of bringing some human perspective and connection to the horrors that Saruman was wreaking on Rohan. Why could they not have used Beregond, and his son Bergil, as a way to do the same thing in Minas Tirith?
Aragorn in the Houses of Healing. I hated to see this go, as more than anything else this was how Aragorn proved himself to be the true King, but I have to admit that it didn't leave a noticeable hole in the flow of the story. I've heard there will be a scene with Eowyn and Faramir getting together in the extended dance remix, er edition, which is good - Eowyn disappeared a bit too quickly as it was. Yay, I killed the Witch-King, okay, now go hide in a closet 'cause we don't need you anymore.
The visuals of Minas Morgul and Minas Tirith. Hot damn, those were *perfect*. It's odd - I actually hate Alan Lee's art, as it's all so washed out and (to my mind) lacks the vibrance and solidity of Tolkein's world, but when brought to screen his visuals really work. I am impressed.
That covers a fair bit of my thoughts, I think. I'm now going to go reread the book, hopefully to reshape my memories into the movies that they could have been....