The Black Cauldron is the worst. Can't say I liked any bit of it.
Atlantis runs second, there are some entertaining moments with some cool ideas, but really kind of an odd story where none of the moments aiming for the heart really worked.
On a side note, the movie I most expected to dislike but ended up appreciating was Treasure Planet. Here's a movie with terrible box office, but I actually thought it was pretty well done, great 2D animation mixed with CG effects, and the Jim Hawkings/ John Silver relationship was pretty effective. Hey, it even scored a 72% on Rotten Tomatoes. Not bad. It's a shame this film was blamed by Disney execs as the one that killed traditional animated films, but hopefully with the new regime that perception will change.