Wow, swim trunks with that mesh seem like a really bad idea for anything over a mile or two! It'd be embedded in my skin!
Cycling shorts FTW. Most comfortable, most ergonomic, nobody really cares what I'm wearing even if I did feel self conscious, which I don't.
I tried overshorts and such but just committing to cycling shorts is easier. Occasionally I'll wear the champion briefs mentioned above when shorts need washing. I don't "need" padding for my commute but I do need the right fabric/no seams on my skin.