I continue to wear "green silkies" aka "ranger panties" issued as PT shorts in USMC. You can buy them online from Soffe (look in the 'Military' section). Eastbay.com sells 2" and 2.5" split and half-split running shorts - same ones my college uses and my high school & the local HS cross-country teams wear. Both have liners, but the Soffe brand are still regulation nylon with same nylon liner - standard sizing is fine for most of us "bigger" guys, but if you want a little more support for your equipment, go one size down. The Soffe brand allows a lot of flopping and won't hide even a semi, and certainly shows if you've got a bigger package, so keep that in mind. The liner on the Eastbay brand is a little snugger, but it's still going to show what you've got.
For me, I'm proud of my package and don't care who sees what, even like to show it off whenever possible (and at least semi-appropriate)!