Petey's second birthday show is pretty great (02/01/05). So is the one where Tom bashes Lord of the Rings for the first time (02/05/02). And the one where he bashes LotR the second time (01/21/03). I also have a soft spot for the shows where Tom turns an L on its head, like the one where the calls get so bad he just sings Elton John for awhile (12/29/04) and the one where he has to do another three hours and he's so bored he's trying to call phone booths (09/02/03). Speaking of singing, I also like the one where Tom starts singing Bridge Over Troubled Water to Sathington to cheer him up, but gets so into it he just winds up singing the rest of the album.
And I feel like it goes without saying, but the episodes where Wurster comes in are in a league of their own, particularly the one with Paul F Tompkins.