Sam Harris is my top pick. Along with Sean Carroll who's a physicist. The atheist experience, the thinking atheist, very bad wizards, intelligence squared... all amazing podcasts.

Thanks for posting this. I just made a list of things to do, and find new podcasts was near the top. I look forward to checking out the suggestions.
S-Town was an interesting listen that I would recommend.

I would have to mention "The Skeptics Guide to the Universe". It's a panel discussion, they give the skeptical/scientific perspective on news. They keep it pretty light and easy to listen to.

Most of you know the Sam Harris/Waking Up Podcast. Great for more heavy topics. Many of the shows are very fascinating.

Radio Lab, Malcolm Gladwell’s revisionist history, TED radio hour, smart drugs smart (neuro science) Pod Save America, Rachel Maddow, Larry Wilmore, Preet Barara

A couple I have been listening too lately are:

Women Beyond Belief (http://womenbeyondbelief.com/)
The Atheist Experience (http://www.atheist-experience.com/)
The Non Prophets (http://www.nonprophetsradio.com/audio/)

I've got my podcasts so that each day a new one is uploaded so I never run out of them to listen to. My favorites are the friendly atheist, talk nerdy, sceptics guide to the universe, cognitive dissonance, God awful movies, scathing atheist and the wellred podcast

I really like NPR, especially Wait...wait...don't tell me. I find it very smart and funny and I'm a sucker for both.

I love Seth Andrews. I believe Aron Ra has a podcast. He is good. Sam Harris is another.

I’ve wondered the same, found the same, but not really any other that seem worth my time listening to… The Thinking Atheist, to me, can sound a bit full of himself … but has a great media presence, and ultimately, his messages are good. There were a couple of other guys, sounded like a very loose forum of sorts that, to me, went nowhere.. I think it’s a major niche in need of filling!

I like that one. I just started listening to The Atheist Pastor. He's local to me so it's comforting to know I'm not alone. Otherwise, I listen to nerdy science podcasts...SpaceTime with Stuart Garey (sp?0 is my fave.

Friendly Atheist is good also. Science Enthusiast is ok, but the male host tends to talk over and mansplain to the female host.