Well Zach got it mostly right. My setup has gone through a number of revisions (an is about to go through another one before the next episode), but the basics are this...
I use an Audio Technica AT2020 (http://www.sweetwater.com/store/detail/AT2020/
) through a USB audio interface (MBOX 2) that is recorded directly into Pro Tools.
Zach uses that Samson G Track and we hold the conversation over Skype. I then use one of two programs to record the show depending on which computer I'm using. On the Mac, it's Audio Hijack Pro (http://rogueamoeba.com/audiohijackpro/
), and on the PC it's PowerGramo (http://www.powergramo.com/
). The key with either is to record the incoming audio and Skype's audio on different channels. This allows you to do separate equalization and compression on the voices.
After all is said and done I pull both files, as well as all of the themes, cut music, and any clips, into Pro Tools to do the edit. There are a whole slew of programs that are good for editing shows...I know a lot of folks who use Garageband, Audacity, or even Adobe Audition. As an audio engineer by trade, I feel most at home in Pro Tools, and use that despite some of it's "downsides" like its slightly steep learning curve and real-time bounce.
There are two keys to clarity in audio that go beyond mics or the program you use to record: internet connection and post processing. When recording over Skype, it's vital to use a wired connection and be sure to close any programs that use a lot of bandwith (torrents, iTunes, etc.). The second is the post processing: equalization and compression. I could go on and on and on about the details for these...so let me know if you're looking for specifics.
Hope that helps!!