I posted this in the TATV thread, but Io9 has posted an amazing compendium of meta-story telling in television, with references to everything from Mister Rogers Neighborhood to Trek and The Simpsons.
The commentary section is chock full of wonderful examples. Some of my favorites:
The DS9 Episode with Sisko as the SciFi writer dealing with racism
The end of the 80s Show Newhart and also St. Elsewhere
Glee's habit of writing dialogue to respond to fan criticism and commentary
Supernatural's storylines about fan culture
Buffy's episode where Buffy is a girl in an insane asylum
Xena's episode about the making of Xena, with the cast playing asshole versions of the showrunners
There are so many examples. Anyone have favorites?