Unfortunately I'm stuck doing Yahoo since that's what 95% of my league (my friends league) likes to do. We just do a redraft every year.
However, I did a football in Fanball.com last year and liked it. They also have a baseball "commissioner" program. It's $50 and you can do just about anything you want with it (rules, scoring, keeper, etc...). I've only ever done Yahoo and Fanball and I would recommend Fanball. I'm actually hoping to get a baseball league going with fanball next year myself but I'm obviously going to have to find another group besides my friends
. I've never done a keeper or dynasty and would love to try one.
Check out Fanball.com baseball commissioner.