Most of my leagues are yahoo leagues, and I think they have a stable and easy-to-use setup for a free site. I usually have multiple leagues here, so I don't mind paying the $10 for live scoring since it extends to all of your leagues. (I just wish I could have more than 4 teams per screenname)
I have also used nfl.com (same as sportsline), espn, foxsports, sporting news, and fleaflicker.
nfl/sportsline - decent setup and lots of cool extras like uploadable team icons and automatic linking to research and news, but I had some difficulty adjusting to the nuts and bolts of it since I am used to yahoo leagues. nfl.com is the free version with free live scoring.
espn - it was an ok site, but they make you pay for the ability to do detailed research on players. Live scoring is not free.
foxsports - was so bad in '05 that I swore to never use it again. They had free live scoring, but it did not update very quickly if it worked at all, and they would routinely roll out a site update that would erase transactions. It may be better now, since '05 was their first year, but I don't care to find out.
sporting news - switched to them mid-season because of the inadequacies of foxsports. It was a very good site, but I would expect that out of a pay site. I liked it more than nfl.com/sportsline, so if I were going to pay a fee for a league management site, I would probably choose them over sportsline.
fleaflicker - I think it is fairly customizable, and I thought it was good for a free site with free live scoring, but it was difficult to use it for player research as their wasn't very much useful information. The draft room was good, too, but I would suggest using another site for news and player research if you decide to use it for a league.