LotR of course, but then, we are talking about Tolkein. Fellowship was the best movie I'd ever seen at the time, bar none, and I was very disappointed that it only got 4 academy awards (course, this was the year Halle Berry (Monster's Ball) beat out Nicole Kidman (Moulin Rouge) so I'm pretty sure they were on something). The extended versions topped the originals, and the follow up movies were as good, if not better than the first.
As for the Matrix, the first one was excellent. Unfortunately it went down from there. At the end of the first, Neo had apparently become a virtual god, yet for some reason he felt the need to fight everyone hand-to-hand... please.
The second one was ok, but overdone. The battle with Smith was far too long and the overuse of stop motion was crap. Frankly the slowing down aspects are good to show things that move too fast for the human eye to see (the gunfight with Trinity falling worked well), but to slow it down just to vogue out is stupid. Then there's the whole rave scene with Morpheus changing from the soft-spoken, well dressed leader of a special group of techies into some tribal shaman just wrecked him for me. Mind you, if you edited out about a half hour or so of the movie, it could be much better.
I prefered the third to the second, since some of the aspects that made me dislike the second were toned down in the third. We had more focus on the literal battle between Zion and the machines along with Neo and Trinity going off to face the machines directly. Apparently unlike many others, I didn't have a problem with the ending, since time marches on and there are other people's stories to tell...