podcasts
 
Atheism/Humanism/Reason
Point of Inquiry Podcast of the Center For Inquiry (CFI)
Great. A bit too much Paul Kurtz, but I think they do that when they can't find a guest.

weekly
The Atheist Experience The audio from The Atheist Community of Austin's tv program.
The only problem this show has is its rotating co-host schedule. Some of the co-hosts are not as good. Look for Jeff Dee or Russel Glasser. Avoid the Russel's sister.

weekly
The Non-Prophets
The Atheist Community of Austin's audio podcast.
Consistently good.

bi-weekly
The Skeptic's Guide to the Universe
New England Skeptic Society's podcast. 
Ok, but these are conservative, ideological Libertarians (in the American Libertarian Party way). Too bad they keep their political and economic opinions protected from the skepticism they express towards everything else.

weekly
A Christian and an Atheist
"The show where two friends debate God, faith and morality"
Decent. At first it may appear that the atheist is pretty weak. Give it some time. He's not bad.

irregular
Skepticality
Official podcast of Skeptic magazine
Disappointing. The hosts seem void of energy or passion. 

irregular
Humanist Network News
The podcast of The Institute for Humanist Studies (IHS)
monthly
Logically Critical
Critical reasoning and humor.
Even when his arguments are not very solid, it's still funny.

irregular
Richard Dawkins archive
Ola Endre Reitstøen has created and maintains a great freethought archive of links to mp3s, and streaming audio and video.
Too bad they all aren't mp3.

n/a
Daniel Dennett archive
Ola Endre Reitstøen has created and maintains a great freethought archive of links to mp3s, and streaming audio and video.
Too bad they all aren't mp3.  
n/a
 
Science 
Evolution 101
Zachary Moore tries to explain evolution to non-scientists.
irregular
Scientific American
"Join host Steve Mirsky each week as he explores the latest developments in science and technology through interviews with leading scientists and journalists."weekly
New Scientist
New Scientist's weekly podcast
weekly
Science Friday
NPR's weekly audio show
weekly
Seed Magazine
Seed Magazine's podcast
weekly?
Science & The City
general science podcast
irregular
Berkeley Groks
general science podcast
weekly

Other
Democracy Now
The best non-corporate news source
daily
Tech Nation
occasionally has an interesting guest
?
Hansel Minutes
.NET developmentweekly?
Polymorphic Podcast
.NET development
irregular
Counterspin
FAIR's podcast
weekly
Media Matters
Bob McChesney on the media
weekly