I want to listen to that one again. Even though the mechanics they're discussing are outdated, a lot of the discussions are still relevant. Like you said, Mike Krahulik starts the podcast saying "I've never been through this 'new edition' thing. I don't understand why I need a new edition." and later on he seemed to come around.
Oddly enough I don't think I've seen a post about D&D on PA since the starter and Basic came out. I wonder if Mike and Jerry decided they'd rather stick to 4th? Either way I'd be interested in seeing what they think.
Didn't they eventually move on to other games systems? I haven't read Penny Arcade in ages but I seem to recall Warhammer or something like it and some form of card/RPG about kid scouts or something.