The last of the advanced features we've introduced in my "primary" fantasy football league is one of my favorites.
Minor League Keepers - Yes, I realize that the NFL doesn't have minor leagues, but the fact that college football players don't get paid (except at Oklahoma) shouldn't keep you from spicing up your fantasy football league.
In our league we have a three-round draft of college players each year. We allow teams to keep an unlimited number of players with NCAA eligibility (encouraging teams to gamble on freshmen and sophomores) but cap the number of non-NCAA eligible players to three. You can have players on your team for only two years. Those are only our rules; naturally you can change them to whatever your own league is comfortable with.
Having a minor league system has significantly increased owners' interest in college football. Before we had this system, college football players only existed in April when Mel Kiper put them on his big board. Now we have discussions about the Outland Trophy and who's leading the SEC in rushing. You know you're playing serious fantasy football when you get emails on Sunday morning talking smack about how poorly Marlon Lucky did the day before.
The minor league system has also given us an appreciation for how difficult it is to project NFL stars a year or two years ahead of time. While one owner has both Reggie Bush and Joseph Addai this year (ugh), nobody drafted Jay Cutler or Marques Colston when they were in college. And while the guy who drafted Adrian Peterson has counted on a future NFL star for the past two years, pity the guy who was basing his hopes on the injured Michael Bush. Oh wait, that's me. Damn.
The minor league system has opened up an entirely new area of fantasy football for our league. It has enough impact to reward those people who prepare (or are lucky) but it's not too overpowering for those who don't like keepers. If your league is talking about new rules for this season, bring up this idea and see if it's right for you.