A system i use in two different leagues that i run and seems to work quite well is like this:
weekly games, maximum 8 players per table
each table plays unto itself, no balancing tables until the FINAL tournament
1st person knocked out gets 1 point, 2nd out gets 2 points etc etc...if there's less than 8 players we award 1,2,3 for the first 3 out, then 8, 7, 6 for the winners etc skipping the 4 or 5 point.
if you play with less than 8 per table, just "slide" this scale, but the most points awarded should always be the maximum you regularly seat at a table.
we accumulate points from week to week, and EVERYBODY that ever played is eligible for the final tournament. At the final, we give $100 (or $200 or whatever) in chips for every point a player has accumulated, and that final tournament is played tournament style (we move players and balance the tables) until there is a grand prize winner...
We've found doing it like this has a few advantages:
1) it doesn't matter how late after the "start" a player joins the league, they still have a chance to win overall in the final...the "one chip one chair" syndrome.
2) one good player who comes one week can be competed with by a beginner who comes every week.
3) everybody who plays is guaranteed at least one point each week.
4) the league can be spread into multiple rooms (until the FINAL, that is). In our case, that makes it easy to separate the smokers from the non-smokers. i guess this also means that the league can be run on multiple nights of the week...never thought of that until just now.
5) one of the leagues rotates the deal among all the players at a table, but the other league prefers one dealer for the night at a table. In that league, the winner of a table MUST deal the following week, and guaranteed a MINIMUM of 4 points for dealing. They may play as they deal, so they don't miss out on playing. If they earn 2 points (2nd out), they get 4...if they earn more than 4 points, they get what they earn. The 4 point bonus is NOT in addition to what they earn, it just guarantees them a minimum. we NEVER have trouble getting dealers! If a winner doesn't show up to deal the following week, somebody volunteers, but we are sure to "spread" the job around so that one player doesn't grab mega-points just for dealing.
i've been running leagues like this for over a year, and the system works very well for us...