Alright, that inspired me to post my top five. I've listened to every episode at least twice (except today's episode I guess) and put an embarrassing amount of thought into this.
1.
Howard the Duck (
#65, Live show with Kristen Schaal)
It would be intellectually dishonest to put this anywhere below #1. I know it's kind of early, but this one is going to stand the test of time. It has everything in great quantities. This is unquestionably June's best episode, and one of Jason's better live performances. It's 89 minutes of joyful insanity. A tour de force of deconstruction.
2.
Sleepaway Camp (
#48 with Zack Pearlman)
As Polka said, this episode is in a whole world of its own. It takes everything in their power to break things down, but with this film their analytic skills hit something of a brick wall. The results are sort of mindblowing.
3.
From Justin To Kelly (
#57, Live show with Nick Kroll)
Jason is in absolute top form in this live episode, and that's really all it needs to become a classic. In some live episodes he tries a little too hard (Anaconda), but he gets it just right in this one. Also features the most thorough and engaging wardrobe discussion of any episode.
4.
Stop! or My Mom Will Shoot (
#61 with Kate Spencer)
This is definitely one of the most fascinating episodes they've done. They discuss screenwriting theory, gender politics of the early 90s, suicide fixation, the sexualization of babies, and the movie's many oedipal themes. Plus a few things I dare not spoil.
5.
Barb Wire (
#46 with Jesse Thorn)
I'm pretty sure Jesse Thorn is my favorite HDTGM guest. He's sharp as a tack, as they say, throughout. But June shines in this one too. The feminist discussion (which sort of spans the whole episode) — or as Jesse Thorn calls it, "Barb Wire in conversation with Naomi Klein" — is priceless.