Hmm, I don't think I've even finished or found all the quests. But out of the ones I've done I'll list my favorites in no particular order.
Tranquility Lane: Loved the whole 1950's American Town simulation. The sociopath inside me will always enjoy torturing the residents.
Stealing Independence: I can imagine that if Indiana Jones lived in an Apocalyptic America, he would definetly join me and Sydney in trying to steal the Declaration of Independence. Exploring the National Archives was pretty damn cool, and I love the robot.
Wasteland Survival Guide: For some reason I love working for Moira, I guess because I agree with her whole reason for writing the Wasteland Survival Guide. Plus it gives you some nice rewards.
Power of the Atom: The first real quest I did in the game. I've done both sides of it, but I think I perfer blowing up Megaton because I like the house in Tenpenny Tower better.
The Velvet Curtain: The only quest I've really done in Point Lookout, but it was fun. I loved walking in the footprints of a Chinese spy who died over 200 years ago.