I've always felt that Yahoo has the best Fantasy Football system. Haven't tried NFL.com's recently, though. But it seems like Yahoo has the best combination of features, presentation, and options. They seem to be ahead of the rest of the pack when it comes to adding new elements, too.
We did ESPN last year in one league, and it had some obnoxiously bad webpage design in a few areas (and at the time, they were charging $5.00 for their mobile app!).
Edited, Sep 18th 2011 10:07pm by Eske