The ramblings of my disordered mind:
Good Stuff
My favorite part had to be the charge of the Rohirrim: I didn’t find the movie as emotional as most people but I teared up at this point, it was so bloody cool.
Sam is the f’ing man.
The coming of the eagles was also very moving, though I thought there should have been more of them
Minas Morgul and Minas Tirith, as most have said, were positively stunning.
I too liked the bit were Sam is sent home, but then reutrns to save the day. I like how they didn’t show Sam taking the ring from Frodo (at least if they did, I missed it), so you sit there wondering (even if you’ve read the books) “what’s going to happen now?”
Paths/Host of the Dead: Awesome. It would have been great if they could have gotten Geoffrey Rush to be the King of the Dead. Oh well. 
The Battle of the Pelannor was unbelievably cool: I didn’t think it was really that long at all.
I like Pippin’s song (and felt bad for him! poor guy…), and Aragorn’s as well. As a side note I felt that there was a lot stuff for the book fans: Aragorn is said to be Elendil’s heir, whom they’ve shown but never really mentioned by name; what Aragorn is actually signing about, “The Eagles are coming,” etc.
Okay/bad stuff
In the Two Towers, Frodo shows the Ring to a Nazgul at Osgiliath. In RotK, after Pippen looks in the Palantir Merry tells us Sauron thinks Pippin is the Ring-bearer. Huh? Did the Nazgul forget to report the Ring, or something? I think I need to see it again; maybe this will be a little clearer to me.
I actually didn’t mind Legolas and the Oliphant, since it was pretty brief and Legolas didn’t really have much else to do (and Gimli’s reaction was great!!)
Eowyn: “I want to save you!”
Theoden: “You already did”
Anakin Skywalker: “You were right about me…tell you sister…you were right…”
(I still liked the scene anyway)
The “Pippin Shuffle” when he has the Palantir was a little silly.
Minas Tirith looked way too “fixed” during the coronation: they show what it looks like as they ride to the Black Gate, but it would have taken months or years to fix all of that up. They really give no good indication of time at that point.
I thought the Crown of Gondor should have been tons cooler: instead is was a little plain, much like something a King of Rohan would wear, and not one of the cool helms of Gondor (like what Faramir wore or the ones with the big wings like the Guards of the Citadel had).