My very first NCAA 2004 league was a bunch of Gone Gold guys making one. Unfortunately it didn't last longer than a month, but it was a great start. Since then I've gotten into, commished, and started several great and clean (no cheese/cheating) leagues.
CSFL - 70 team league. I'm the rules commish there. Traditional conference setup. Waiting for 2005 to come out, but there is an off season league.
XSFL - 32 NCAA teams in an NFL style setup and schedule (mid majors work awesome for this format). The smaller league allows it to have the best cleanest coaches (not necessarily skill wise though. Many like to play for the fun, win/lose). www.freewebs.com/xsfl - It's currently running.
Once NCAA 2005 (PS2) comes out both leagues will be up if not going right now. These are 2 of the best out there. Other notables are PCL, OCFL, INCAA, and NDL.
You can find me on AIM(jamesthecarman), or e-mail [email protected]