Are you using Sportsline Commissioner?? IMO It's by far the best and very user friendly once you get used to it....you can personalize the home page also which I like.
Fanball.com Commissioner -- I think it's only $50
TQstats.com -- $100 I think, but I hated it
Real-time Sports (rtsports.com) -- $75 early bird I believe for Gold package, $135 early bird for Platinum package (allows for the same player on teams)
There are quite a few others, but Sportsline Commissioner is the best IMO. Nice page designs and very user friendly IMO.