Pottery Barn shows classy ways to do a themed boy's room. They pair classic furniture, patterns, and colors with themed accents.
Land of Nod has similar examples. I really like this idea since I asked our 4-year-old what kid of room he wanted and he said Transformers. It's nice to see how a room can be fun and not "overly-themed". It also makes switching things out when your child changes interests a lot easier.