My roommate has made some of the best beer cheese soup I've had. He starts with a rue, adds a few kinds of cheeses (cheddar, gouda, and fontina I think were the last three he did) and then adds beer to get the right consistency. Usually a pale ale is best, or even an IPA. The rue really makes a difference when trying to get the cheese to not separate. Then, depending on what you're going for, you could add green onion or bacon or something, but that should get you where you want to be. It really is all about the cheese. The better the cheese, the better the soup.
As for specifics, I don't have a recipe, because he pretty much cooks whatever he feels like and just adds stuff on the fly.