Commando is the way to go and I second the compression short advice for long runs, prevents chafing up high if you're built with bigger thighs. If you're not using compression shorts use body glide if chafing is an issue.

I have a pair of Lulu Lemon shorts I love because they are snug enough to stay in place and prevent chafing but they are also loose at the leg hole opening making them more like a regular short. That makes me feel a little less "revealing".