Well, i have my own system, and it's usually mental with me, but...
I like to rank by position. It's a more standard way to compare depths by each spot. For instance, slugging first basemen are easier to find than a slugging second baseman. As guys disappear off the draft board, you want to cross out those who are picked (obviously) and look at depth.
But don't make the mistake of beign driven by depth, either. Pick those guys who are good value at the spot.
Also (and i may get some people who disagree with me on this), i throw out some guys altogether, those whom i will not draft under any circumstances. Guys like Steve Finley, Sammy Sosa, Magglio Ordonez for next year. It works, believe me. If you're in a keeper, don't feel ashamed to reach a little for a young guy who's about to break out.
Just a few things i employ. It worked for me this year, i finished in first.