I'm extremely partial to the Haunting of Harrowstone. However, like with all Paizo adventures I've been involved with, it plays much better if you're willing to dump the gimmicky module-specific mechanic. In this case, that means the trust mechanic.
We Be Goblins! is my favorite Pathfinder module we've run because it was so much fun to play the goblins. As I was thinking about the Paizo modules I've really liked when I looked them up they were all pre Pathfinder.
Do you want just Paizo stuff? I don't think I've played enough published adventures to give anything more than 'oh that one was fun' but being fun isn't necessarily the 'best'. If I include those I've read, maybe that would help.
What about Rappan Athuk? I've never actually played the Pathfinder version and we never got out of the 1st module when it was published for 3E, but it was fun and flavorful.
Perhaps this bump will remind people who can post more useful ideas.