Bible Geek - "Theology with a twist but without the spin." Robert M. Price is one smart guy when it comes to interpreting the Bible and a prolific author but the sound quality of many of his early podcasts are excreble and I find his delivery frequently grating. Price can also be heard, in a more moderate style, as a frequent host on Point of Inquiry.
Irreligiosophy - "The one true podcast." The unhappy young men behind this atheist podcast were once disaffected Mormons who have since seen the light of reason. Much as converts make the most fervent religious zealots, disillusioned Christians frequently make the angriest atheists. Their vitriol might be tolerable if they didn't strive to earn their iTunes [Explicit] rating every time they opened their mouths. Swearing for it's own sake isn't shocking (except maybe in Utah), it's just boring.
Skeptic Zone - While it's interesting to hear the Australian perspective from the leaders of the skeptical community there something about their conversational tone just doesn't grab me.
[UPDATED TO ADD: As of October 2010 I'm giving Skeptic Zone another try.]
Reality Check - This podcast by the Ottawa Skeptics is nice enough but the topics covered are dealt with in greater detail on other 'casts.
The Infidel Guy Show is the oldest skeptical podcast on the web. It deals with religion as well as the paranormal and pseudo-science. The production values can be a little rough and more than a few podcast debates have raged out of control of the host. After 11 years the host and producer, Reginald Finley, is taking a break.
All of these can be found at their respective websites and at iTunes.