Hmmm... I have toyed with the idea of going commando before. But, since to date I've dove mostly on lakes, on small boats without private heads or cabins for changing, that has always seemed like a bad idea. Additionally, I could imagine being rubbed raw or developing a rash *down there* after a few dives.
I've been wearing a pair of Lycra surf shorts (some may call them rash guards, swim shorts, bike shorts, compression shorts, or whatever). They are extremely comfortable and don't show too much in the groin area, even though they are skin-tight. Board shorts (swim trunks) tend to bunch up on me and drive me nuts.
When I am swimming at home, alone in the pool, I usually wear very tight Speedo-style numbers... I never dive with them, though, since I am typically with "family-friendly" groups that don't want to see my junk, ROFL. I'd totally do it, though, if I were in a more private dive setting. Seems like that would be the most comfortable.
I wear a pair like these... they are very comfortable. Might check into something like it.
Mares 6oz Trilastic Rash Guard Shorts 482054 with reviews at scuba.com