Hi Chris,
Here's what we do in our league. I'll try to keep it as short as possible, but it is a pretty interesting system.
Each player is divided into one of four "Tiers" based on their average points per game from the previous year. Each player then has a "round" cost as well as a dollar cost. Every team will have a varying amount of players in each tier. The championship/play-off teams generally have more Tier-1 and Tier-2 players than non-playoff teams. Each owner will have to choose how many players he wishes to keep.
Tier-1 players make up the top 10-15% of players. Each owner is allowed to keep only one Tier-1 player. If an owner keeps a Tier-1 player, that player becomes his first round pick in the draft and also costs between $300 and $600 of his total player acquisition money. Each owner only has $3000 for player acquisition money for the entire season and this includes blind-bid waivers as well as keepers, so your Tier-1 player can be a significant investment. Also, by limiting each team to just one Tier-1 player, most of the best players are thrown back into the draft, which keeps drafts from becoming boring because most of the best players are kept.
Tier-2 players make up the next 10-15% of players. Each team is limited to keeping two Tier-2 players. These players cost a little less and if they are kept, will also cost rounds 5 and 6 of the draft.
Tier-3 players make up the next 20-25% of players. Each team can keep up to three Tier-3 players. Again, these players are a little less expensive but if a team keeps three of them, it costs rounds 10, 11 and 12.
Tier-4 players make up the bottom 50% of players and cost the least to keep. About $40. Each team can keep an unlimited amount, but each player costs a round beginning at round 20.
This system was born when our league had a real difficult time deciding on the total number of keepers we could keep. Half the league wanted to keep a small number so the the draft was still exciting. The other half wanted to keep a larger amount, shortening the draft in time and rewarding the effort put into roster building. This system was the ultimate compromise as each owner is limited only in the amount of money he wants to spend and how many draft picks he is willing to fore-go.
As commish, it takes me about two hours of work to tier everything out and then another couple of hours to put it into an easy-to-read spreadsheet and send it out. I try to get it done as soon as possible after the season ends. It does lead to some interesting trades in the off-season. For example, let's say a team has both Aaron Rodgers and David Johnson. Both are Tier-1 players and the owner can only keep one of them. He can try to trade one to another team that has fewer (or worse) Tier-1 players, but might have two or three high-potential players in lower tiers. The possibilities are pretty endless.
Let me know if you need any further info about it.