Three top previously-unmentioned candidates (in no particular order):
-August 18, 2009: PATTON OSWALT Gets Metsmerized Live In The Studio! A Caller With A Cursed Family. Matt Fraction Gets Interviewed By The Tombstone Kid And Larry Da Perv Requests A Radio Date With Laurie! (That "Get Metsmerized" bit is maybe one of the funniest things ever deconstructed on the show. The rest is just gravy. Really good gravy.)
-October 3, 2006: Bryce And Reagan. PC Richard. Sam's Town. Atlantic City. The Scary Neighbor. Jim Cramer. The Children Of Ritalin. (I don't know why entirely, but the "Tom creates lyrics about shoplifting and sings them to the PC Richard theme" bit absolutely killed me.)
-November 28, 2006: Pudge And His Reading, A Local Man With Some Money Issues, Talk Of Happy Feet, And Some Of The Worst Callers In The History Of Radio. (Better known as the episode where all those defensive Tom Waits fans call in and "Best Show Law" is established. Also the first episode I listened to where I really "got it" -- I listened to the 10/3 episode later, and before that I mostly just knew about the S&W stuff, which I loved.)