When autodrafting, you should always exclude players who are out for a significant portion of the season. Because the rankings are based on the prior season's production, players who did well will be ranked highly regardless of 2007 projections.
This also works in fantasy owners favor when the player in question has no prior season performance to rank highly. The obvious one right now is Royals 3B Alex Gordon (#907 out of 1,013), but all rookies with little-to-no prior year numbers will be ranked near the bottom of the rankings. In addition to rookies, the pitchers who are slated to close in 2007 but did not in 2006 will also be under-ranked.
Given a 16-team league with a standard Yahoo! settings will only take the top 326 players (21 rounds * 16 teams = 326), any players ranked below that number will be left in the pool (assuming no team changes the pre-rankings). This is why there are so many good players in the pool after the autodraft runs - the rankings did not consider projected 2007 values.
To better rank your list, move some of the players on the list below into your pre-rankings. At #907, Alex Gordon would never be autodrafted if no teams adjusted the pre-rankings. How high should you pre-rank him? That I do not know, but, for reference, Devil Rays' OF Delmon Young is #97.
And what is up with Indians' 3B Andy Marte being ranked 999 out of 1,013?!?!?!