I tried a bunch of the free sites last year to compare, and yahoo is still my go-to site for free fantasy football. The interface is simply well done. I especially like the watchlist, which is a feature missing from a lot of the other free sites.
ESPN - also nice interface. Lots of linked info and articles, which is a plus.
fleaflicker - good interface as well. I like the prominent info about percentage add/drop for each player week to week. Gives you a good idea of trends. Not the best place to get a random public league going, but ok if you have guys in a league just looking for a site to use.
cbssports - dunno what the differences are between the free league and paid league. It works, but nothing spectacular.
fox - awful buggy website. maybe they've improved it, but putting something that bad out there the past couple years does not inspire confidence.
If you're willing to pay, I'd recommend MyFantasyLeague over cbssports.