Rationally Speaking is IMO the best thing out there around 80% of the time. The other 20% of the time they delve into straight-up philosophy which, I'm sorry, is mainly BS. That being said, Massimo Pigliucci is easily as much of an expert in his field (biology) as Dr. Novella is in his and has written a couple of skeptically-inclined books as well (particularly Nonsense on Stilts).
My list changes from time to time, so what the heck, here are the 25 which make my cut:
Cognitive Dissonance
Common Sense
Hardcore History
Inkredulous (at least in theory; I actually haven't listened to this yet)
Monster Talk
NPR: It's All Politics
NPR: Planet Money
The Pod Delusion (see comments on Inkredulous)
Rationally Speaking
Schlock Treatment (now with extra unjust mockery of Johnny Slick!)
Skeptics With A K
Stuff Mom Never Told You
Stuff You Missed In History Class
Stuff You Should Know
Tech Stuff
The History of Rome (mostly I've been working through the archives on this... up to Trajan)
The Reality Check
SGU
Thinking Allowed
Thomas and the Bible
WBUR-FM - On Point With Tom Ashbrook