I'm in the camp that thinks the extended versions of all three films are superior to the theatrical ones, even if they do end up introducing some fluff here and there. Having read the books I know that fluff is something like 20% of what's going on in anyway so it doesn't bother me at all. So overall, I know how crazy the production was and found that they did an amazing job with what they had to work with.
Except for one thing.
The one thing that is just unwatchably bad to me every time I revisit these films is that scene in The Two Towers when Gollum talks to himself. There are a few things he does that irritate me but this scene is the pinnacle of it. I know that, much as with the eye of Sauron, they wanted to visualize a concept that was handled through internal narrative in the book but trying to make Gollum's struggle into something "funny" was absolutely the wrong choice. The worst line out of the entire sequence is where he goes "You don't have any friends, no one likes you!" all sarcastic-like. It looks silly and I didn't appreciate what could have been an interesting, dark moment into a goofy piece of computer animation.
And in case anyone takes issue with my interpretation that it was supposed to be funny, well, I'm forced to think of it that way because of my experience with seeing the movie in theatres. At the time, I must have hit a perfect storm of timing with my friends because due to all these crazy circumstances I saw the movie in theatres five stinking times. Each time (and these were all in different cities, too) the audience laughed uproariously during this scene and it just grated on me more and more that Gollum was seen as an opportunity for comic relief. He's sad and piteous, not a clown.