I use a combination of things, my own mess I came up with. I use K, BB, HA, ER, IP, HRA and Wins for pitchers and R, RBI, BB, AB, K, 3B, SB, TB for hitters. They are turned into scores to calc control, dominance, consistency, power, speed, eye, contact, etc.. I know I use Wins and RBI that could mess up the system because they are not earned simply on a players merits, but they do help to weed out poorer players sometimes.
That is just the stats. I also take into consideration signing bonus/draft status for new draftees and my previous seasons rankings for the rest.
That's where I'm at with these lists. After this, I will put my own spin in on these guys to move them up and down. My goal is to not have to adjust much after the 1st run, but that may take a while.