Padded bike shorts! I love the Aero Tech Designs Top Shelf ones. Expensive but fits and feels great and breathes well.

I wear polyester breathable workout shorts over the bike shorts to conceal the tight look. It still breathes so much better than having any cotton. I like NordicTrack mesh shorts for the top layer because they breathe well and also have retroreflective piping on the sides to enhance nighttime visibility:

http://www.sears.com/nordictrack-dou...&blockType=G21