I went for The Puppet Show because there are only two mystery episodes in the entire show and both are excellent. Earshot is the other one. Chosen was good but not the best. I would be quite happy to see votes for The Pack - it had a different vibe from the rest of the show and the story and acting were excellent. I thought there would be more votes for Angel but it really doesn't engage my mind like The Puppet Show does.
Prophecy Girl is when it stops being so silly and has a nice payoff for watching the season, so I came real close to that. The Puppet Show was also so very close because it was a perfect blend of funny and creepy all the way through (with a nice twist), and Snyder becoming both fun and love to hate (and the ironic statement of how he wasn't going to be eaten the way Flutie was), and if I just saw the season for the first time recently then I'm sure I'd have gone with this one instead.
But I finally went with the Pack. Not so much the first half, but that ending had a lot of payoffs I liked, and can see Willow becoming more self-confident (but not yet arrogant). (And despite that Giles gets knocked out as he often is, I think his dry taunt to the wannabe hyena zookeeper hurt the zookeeper more than the club hurt Giles).
I mean, I probably should have voted for Prophecy Girl, since the title of the thread says 'best' and not 'favorite', but I didn't. Prophecy Girl is definitely the best one, on a technical and writing level, but my favorite is The Puppet Show, so that's what I voted for