I guess I'll be the first to chime in and say it may be the boxers. I used to ride in boxers, and my balls hurt often. I think it's becuase they just sort of end up wherever (including crushing positions) when you sit down. Sometimes, mine would slip down to the side, and when I'd stand up, they'd get caught under the edge of the saddle. That is one of the worst pains ever (especially on a fixie where you can't stop pedalling to sooth the boys).

Anyways, the point of the story is I switched to briefs (a.k.a. tighty whities), and I've been much more comfortable ever since. They keep the boys high and dry, and prevent unfortunate 'hooking'. PLus, my girlfriend thinks they're cute.