The Sam Guevenne's quest is one of my favourite, unfortunately I don't remeber other quests at the moment.
I really liked going through the Volksygge temple, especially the puzzle/riddle I had to do ("One eats this, but fears that"). There was also another temple that I think was part of the MQ which I also had fun delving in.
I quite enjoyed most of the Thieves Guild questline despite it being deplored as terrible! It was fun. I quite enjoyed all of the quests that send you around Dwarven ruins in Skyrim, after hating them almost invariably in Morrowind.
I enjoy Skuldafn after level 30, when the majority of draugr are deathlords.
http://s142.photobucket.com/user/Enoil/media/DarkFishyStick.jpg.html
I can't even remember most of the quest I've done...hmm.
The Dark brotherhood story line was fun though!