As the name says, I'm commando full time. I have been since I was about 15. I saw my father doing it as well as my uncle and decided I would try it. I'm fairly average in size and do hang a little but it has never been a real problem. Luckily, in my career, we wear a robe when we are in front of a large group of people so even my circumcised nature doesn't show through completely.
I do, however, wear running shorts with a liner due to chafing and modesty. I personally don't care if I bounce around, but I would hate to offend a congregation member by literally bouncing past her/him as I jogged by. Plus, every race has photographers, and I have enough showing WITH a liner--wouldn't want those pictures out there without a liner.