Another vote for boxer briefs, especially in hot weather. You're gonna sweat down there anyway (at least I do -- my secret shame). ;vD Thus, you need something to wick the sweat and prevent any skin-on-skin contact. A good boxer brief like the Ex Officio fills the bill.
I actually prefer to go commando style (ha! new term to me) in the spring and fall when perspiration is less of an issue. In winter of course, the base layer serves several functions besides warmth.
Funny story: I used to wear my BPL Thorofare pants "au natural," but my wife laid down the law: Those pants use terribly thin material, and people do stare.