Bloodmoon was my Favorite, as i rather liked the setting, plot, and Werewolves.
Plus, Hircine was, of all the MQ enemies, the coolest. He had the voice, the look, and a bunch of kickass minions.
Morrowind's come second, just because its pretty cool and complex, you gotta love the storyline.
Tribunal is last, though i rather like it, i dislike how it seemed to be made to be played after the MQ.
Not to mention Almalexia was pathetic compared to my Khajiit, he backed her up to the wall with Trueflame and then smashed her to mush.