I have a few favourite quests, such as Zero Visibility, A Plot Revealed (Mage's Guild), Paradise (Main Quest), Paranoia, and the best quest in the game, goes to:

The Ultimate Heist (Thieves Guild):

This is just such a great quest, it has hard enemies, puzzles, times when you have to really think of what to do, makes you amazing at sneaking, and has a great climix, and reward

Yes, The Ultimate Heist was pretty epic(I even learned a little trick to keep my boots after the fall).

However, the miscellaneous quest dubbed "Goblin Trouble" had to be my favorite. I rather enjoy seeing those goblins war with each other and completely ignore me as I go to steal that Goblin totem.

yea thats a good one

Whodunnit has to be one of my favorites for sure. Just, it's simply amazing, with so many ways to do it. Heck, It's got more ways to beat it than Fallout quests do. And that is saying something. Haven't gone through it enough to have done all the options it has. Also, as previously mentioned, Zero Visibility the Goblin Tribes, and of course The Thoronir one. Done that one so much I know just how to exactly do it, but my characters never know.

Sanguine, the quest. That's some hilarious stuff.