I had leagues on ESPN, CBSportsline, and Yahoo this year. Out of these three, I thought CBS was the best (we did the private league, where you have a comissioner that sets up all the scoring rules, roster requirements, etc.). I think the cost came to about $10/team.
The league page for CBS was clunky, but the waiver process and live stat updates were great (on ESPN, the waiver process sucks, and fumbles aren't calculated until the following day). Yahoo is free (if you don't want live scoring), but don't try and change your lineup 5 minutes before kickoff (bandwidth problem).
I've never tried fanball, but I've heard good things.