If you want free league managers for a private custom league your choices are FoxSports (miserable), ESPN (average), AOL (average), Yahoo (good), Fleaflicker (good).
I've used them all in the past (4 years at Yahoo). I tried out Fleaflicker last season and I've been impressed. It's relatively new but it's improved a lot, even in one year. I believe Yahoo is the only one of those that makes you pay for live scoring.