I've been in a Yahoo fantasy baseball keeper league for years now. Here's the way that we do it:
16 categories (half pitching and half hitting). We use mostly standard cats (R, HR, RBI, BB, SB, TB, AVG, SLG, IP, W, L, SV, HLD, K/9, ERA, WHIP)
Each year each team keeps 8 players of their choosing.
Those players are drafted in the managers first 8 slots the next year (which we setup before the draft on Yahoos draft settings page).
Then we draft like normal but the order of the draft is determined by how the teams finished the year before. The last place team gets first pick and the championship team gets the last pick.
There are a couple of other little details but I won't bore you with them. Good luck with your league!