Split vote here.
When wearing bike shorts - commando. But why wear them?
I use UnderArmour HeatGear compression shorts. I wear them under normal shorts or pants or whatever, can ride forever, and still look like a normal human being when I get off the bike. The question for me is not "what do you wear under the bike shorts?", it's "Why are you wearing bike shorts?". Yes, I have a pair or two left somewhere, but that's just not how I want to ride. I just don't do it any more.