You might want to check out Arcadia[0], a Clojure library for Unity game development. It's all done with ClojureCLR and it's pretty cool. Not saying you want to do game development, but they've definitely got a working product and you can see how they've set up their project.
They just got a round of funding this year, and they've got several good talks posted on their homepage about the quirks of working on .NET.