There are so many now that i can't really tell
Any way those are probably my top 5 currently. In no particular order.
Into the pit: Maybe the first quest that used locations in a really different way, the torch mechanic is also a nice touch and really thematic too
The Battle of Lake-Town: A great boss fight, the Smaug deck makes him feel alive and kicking. The burn mechanic also a great thematic touch
The Fords of Isen: A great heavy combat quest.
A Knife in the Dark: What can i say for this one ?!?!?!
Encounter at Amon Din: The best truly innovative mechanic so far (in my opinion)