Things that made me go "Huh?"
* The Beacons — Nice sequence, totally unnecessary to the story. In the book, the muster of Rohan occurs before the beacons are lit. The Rohirrim are already coming. Denethor doesn't know this, so he lights the beacons, but it doesn't change the course of events at all. There's is no reason to show it anywhere but in the EE, especially when you're cutting scenes like Denethor and the Palantir or the Houses of Healing.
* Denethor — Some big changes here, again with the why. He's nuts, but why is he nuts? Because he's been looking into his Palantir. Why didn't Jackson show that? That's far more important to the story than the lighting of the beacons. You also wouldn't need that silly scene where *Pippin* has to sneak up to the beacon and light it. He completely banishes Gandalf from his sight, rather than at least pretend to listen to his counsel, which leads to another silly scene where Gandalf whacks him upside the head with his staff. You don't do that to a head of state, even a crazy one, especially with the palace guard right there! Also, the flying Richard Pryor flaming header he takes off the cliff? Just a bit much, don't you think?
* Osgiliath — In the book, the fighting around Osgiliath is completely offstage. You get after the fact descriptions. I wondered why Jackson would show it. The only conclusion I can come up with is that it's to show the death (by the pig-faced orc, who does have both eyes, BTW) of the one guy who can rat Faramir out to Denethor over the release of Frodo and the ring. Faramir was under a death sentence at the end of TTT, and there was a question of how Faramir could present himself to Denethor in RotK if he's subject to execution for showing up. With his lieutenant out of the way, Faramir just shuts up about the ring.
The other thing here is that the fighting around Osgiliath shows that Denethor is to a certain extent right about his younger son. He sucks as a military commander. His plans are terrible. You don't let landing invaders in behind you, unless you plan to trap all of them. And then it had better be a good trap. You can't take a fortified city back with a cavalry charge. You must lay siege. Is it any wonder all his men are dead?
* "Go home, Sam" — No way Sam would leave Frodo. The whole climb up the mountain (which looked nothing like what I'd imagined from the book) left me going WTF, but especially the whole thing with the lembas.
* The Paths of the Dead — In the book, Aragorn was not nervous about heading out for the Paths of the Dead. In the film he's quaking in his boots until he reaches the tunnel, when he finally discovers some gumption. (I wonder where he found the torch, BTW.) The horses running off bugged, too, although not so much as the fact that they never even called it the "Paths of the Dead" in the film.
* The Lighthouse of Doom — aka Barad-Dur. This got sillier and sillier as the film went on, especially when the eye turned into a toon (thank you alterjess for the image) at the end. All it needed was an "ah-oo-gah" sound effect. There had to have been a better way.
* The cracks of doom — Gollum's final plunge was far too reminiscent of the end of Bored of the Rings, where Frito and Spam push Goddam over the edge to be the anchor. In the book, Gollum slips while doing the Snoopy dance of reclaiming the ring. Frodo doesn't attack him and take him over the edge. After all his pity and protection of Gollum throughout the films, Frodo's now the one that's actually responsible for his death. In counterpoint to the beginning of the film where Smeagol kills Deagol for the ring, Frodo kills Gollum trying to get the ring back.
(One technical thing that just occurred to me. The whole thing of Gollum smiling as he falls to certain death, and then still smiling as he sinks into the lava bugged me. In fact, I don't think he'd sink at all. Lava is far denser than water, far denser than a body. He should be floating on top of the lava, burning to death, rather than sinking.)
* The Black Gate — Why did Aragorn let Faramir come up with the battle plan? Taking your army up there as a diversion is one thing. Standing idly by while the armies of Mordor surround you? The army was way too small, too.
* Elrond — He smiles and sheds a tear when Aragorn and Arwen kiss. Elrond. Does. Not. Cry. There's no crying in Rivendell...
* Arwen — Her life force is bound to the ring? How did that happen? Biggest WTF of the film. Vee suggested that Arwen should have brought Anduril to Aragorn, and joined him on the Paths of the Dead, since Jackson had written Elrond's sons out from that journey. I think I could have lived with that.
There were lots of things I liked.
* Eowyn!!! — The scenes of her killing the Witch King were pretty close to the book, and the battle scenes prior to that show her kicking major ass and taking names. It's a shame the house of healing aren't included, because all of a sudden she's sharing smiles with Faramir, and there's no explanation.
* Sam — Except for him starting to head home, Sam is perfect, especially the bit where he uses his shadow in Cirith Ungol.
* Pelennor Fields — The battle was mostly good. The main quibble I have is that in the book, little of the fighting actually takes place in the city. Gandalf stops the Witch King when he breeches the gate, and the armies of Gondor fight on the field. I didn't mind the Dead showing up at the battle. I thought it was kind of a crime that Tolkein goes to all the trouble to raise the Army of the Dead, then uses them offstage and releases them. I wasn't crazy about the representation (I'd assumed they'd be zombies rather than ghosts), but they were mostly good.
Lots of other stuff, but my memory is starting to run down. I think I need to see it again...