I second the regular bike shorts with baggies of your choice over them. Personally, I gave baggies a try and always got them caught on the seat as I moved back and forth with the changing terrain. Just couldn't figure it out, so I go with plain old lycra. Looks dorky, works great. Funciton over form for me.
When I'm transiting to and from, I throw a pair of gym shorts over them so I can stop and get a drink or snack or whatever.