I don't particularly care about the scoring, but I like the sites that do interesting things with roster construction. Years ago I did (I think) CBS, which had a limit on the number of transactions you could make throughout the entire playoffs. As a result, you really wanted to pick the guys on teams that won, lest you run out of transactions and have to take a zero by the time you get to the Super Bowl.
The past few years, I've done it on NFL.com, which allows you to pick whoever you want each week but gives you a bonus (2x, 3x, etc) for each week you stick with the same guys. So if you pick a guy on a wildcard roster and stick with him all the way through the Super Bowl.
Any other cool variations on that theme?