The Men's Flex Short by Prana. Flex Short: If you're like us, your best days involve several different sports. We built this short with recycled polyester and a bit of spandex for mobility, and added a Coolmax short style liner and a side stash pocket.
I now own three pair of these shorts after buying my first pair on points this spring. They are hands down the best gym short I have found. Fabric is flexible with out looking like a pair of bike shorts, and the liner keeps the boys from being exposed while being comfortable. The price tag while make you think twice, but wear them for a workout and you will never regret it. The side pocket just fits a my cell phone which is a Galaxy S3.
Hands down my favorite shorts that I own. The liner in them is very comfortable and the length is long enough that you don't expose the boys when hitting the bench at the gym. I have even started wearing them on days that I just run. If you like to carry more then a gel pack or a cell phone then they probably are not going to be your top choice. All that said they are still the shorts that I grab when doing anything athletic.