The Memory Palace: This is the way history should be taught, but rarely is. Nate DiMeo takes past events and puts you in the middle of them, in a way that makes you emphathise so much with people from the past. Each episode is a little short story, and they're often only a few minutes long. A great example is this description of when Niagra falls stopped. I have listened to the entire back archive, and want more. Only downside is it's a looong time between new episodes.
The Haskell Cast: Panel discussion with a guest, there is a lot of expertise amoung them and I'm often scrambling to keep up with the barrage of ideas. If this seems too tame, check out The Type Theory Podcast instead..
Benjamen Walker's Theory of Everything: Only caught 2 episodes so far, but they've both been great. Short, punchy, quirky, geeky. Astoundingly good production values.
Lightspeed magazine and Escape Pod blur together for me. Both feature 20-50 minute science fiction short stories, and occasionally other genre fictions. They seem to get all the award-winning short stories. I sometimes fall asleep to these which can make for strange dreams. Two strongly contrasting examples: "Observations About Eggs from the Man Sitting Next to Me on a Flight from Chicago, Illinois to Cedar Rapids, Iowa" and "Pay Phobetor"
Serial: You probably already know about this high profile TAL spinoff. If you didn't before: You're welcome. :) Nuff said.
Redecentralize: Interviews with creators of decentralized internet tools like Tahoe-LAFS, Ethereum, Media Goblin, TeleHash. I just wish it went into more depth on protocols and how they work.
Love and Radio: This American Life squared and on acid.
Debian & Stuff: My friend Asheesh and that guy I ate Thai food with once in Portland in a marvelously unfocused podcast that somehow connects everything up in the end. Only one episode so far; what are you guys waiting on? :P
Hacker Public Radio: Anyone can upload an episode, and multiple episodes are published each week, which makes this a grab bag to pick and choose from occasionally. While mostly about Linux and Free Software, the best episodes are those that veer var afield, such as the 40 minute river swim recording featured in Wildswimming in France.
Also, out of the podcasts I listed previously, I still listen to and enjoy Free As In Freedom, Off the Hook, and the Long Now Seminars.
PS: A nice podcatcher, for the technically inclined is git-annex importfeed. Featuring list of feeds in a text file, and distributed podcatching!