My favorites are the Puzzle in a Thunderstorm podcasts, (GAM, Skepticrat, Scathing), The Thinking Atheist, Serious Inquiries Only, Naked Mormonism, Cognitive Dissonance, etc.
Sam Harris Waking Up Podcast. 'Nuff said.
Waking up (Sam Harris) - very intellectual and thought provoking.
The Thinking Atheist (Seth Andrews) - a very empathetic and compassionate approach, but no punches pulled. Many personal stories.
Cognitive Dissonance (Tom and Cecil) - an irreverent mix of interviews and news coverage - lots of swearing and inappropriate jokes, not for the sensitive type!
Skeptically Yours (Emery and Heather) - similar to Cognitive Dissonance but with more celebrity guests.
Ardent Atheist (Emery and Heather) - see above.
Waking up with Sam Harris, I listen to old episodes of the atheist experience on YouTube ( years and years of content), and I like the thinking atheist.
Non Prophets (when Jeff Dee is on, he's on sabbatical right now)