Several blogs are noticing When Geeks and Stained Glass Collide, a cataloging of the best of the best of geeky stained glass. Most of them have a video game or pop culture theme. Some enshrine science (I like the EM spectrum). All of them are real glass. Yes, somebody painstakingly made that Spider-Man window with two human hands.
For more, but photoshopped, geeky stained glass, try Worth 1000.