I've used Yahoo, MFL, and RTSports. I like all of them, but for different reasons. I'm going to look at Fox and AOL this year.
For my free league, Yahoo has been just fine. Never had a problem getting to the site, making changes, etc. As the commish, yeah it is limited but for a free site, I just want it there when I try and get on line. I don't expect the world and while live scoring would be nice - it ain't all that.
MFL is a little quicker responding most of the time than RTSports. Both are nice. I'm not which is better from a commish point of view as I was just a user both times and they were similar in tools for me.