It's an interesting debate that's highly subjective, because every GM is in a different position. Payroll, owners, competing teams, even luck can all have huge impacts on the performance of certain GMs. But in my mind, there are a few guys that stick out above the rest. They are:
Billy Beane (Oakland) - If you've read Moneyball, you know all about Beane. If you haven't, well, you really should. Beane consistently does more with less perhaps better than anyone else in baseball. He doesn't have a whole lot of resources in Oakland, but the A's are always competitive and usually in the playoffs. In all ihonesty, he hasn't done great with trades recently, but he's a master at picking up the right free agents and does a good job with the farm system.
The biggest complaint I've seen about him is that his teams typically don't perform that well in the playoffs. Well, the playoffs are mostly a crapshoot. In a 5 or 7-game series, the best team definitely does not always win. That's not really the GM's fault.
Terry Ryan (Minnesota) - As a Twins fan, I follow Ryan closer than any other GM. First, his strengths. He runs a great minor league system and constantly replenishes the Major League team with Minor League talent. Almost every important players on the Twins is homegrown. Second, he's great at making small deals. You may remember him making a certan deal with San Francisco, but that's just part of it. He's made lots of small deals for guys like Jason Bartlett, Carlos Silva, Nick Punto, etc. Also, he got Johan Santana in the Rule 5 Draft, and that alone should put him high on the list.
But that's not to say he doesn't have his weaknesses. His free agent signings in recent years have left something to be desired. He likes to keep the young guys down on the farm as long as possible, and that leads him to sometimes going with a lot of veterans that shouldn't be starting. Last year, guys like Tony Batista and Juan Castro got a lot of playing time. This year, it was guys like Ramon Ortiz and Sidney Ponson. That's not good.
John Schuerholz (Atlanta) - If nothing else, just look at all of those division titles in a row. Sometimes people will say he just had some luck in having Maddux, Glavine, and Smoltz, but you can't win that much with only a few pitchers. He did a very good job with the farm system, free agents, and everything else. And again, the Braves might only have a couple of World Series rings to show from all of those division titles, but the playoffs are a crapshoot.
Theo Epstein (Boston) - We all know he was the guy that was the GM when they finally broke the drought. He tends to use a more stats-oriented approach, and that's something I like. But I kind of wonder how he would do with a team that had a lesser payroll. He's made quite a few mistakes, but he can help cover that up because the Sox spend lots and lots of money. GMs like Billy Beane and Terry Ryan don't have that luxury.
Kevin Towers (San Diego) - I think he's one of the more under appreciated GMs but you have to respect what he's going in San Diego. They've been in the playoffs the past couple of years (with a pretty young team) and look to have a good shot again this year.
Dave Dombrowski (Detroit) - Dombrowksi is another guy who I think is a little underrated, as he has had a lot of success in both Florida and now Detroit. In Florida he won 1 World Series and basically built a large portion of the 2003 team that won the World Series. In Detroit he took a team that lost 119 games in his first year, and turned it into what it is now... a team that won the AL Pennant last year and looks like pretty strong contenders once again. Plus, with a young pitching staff the future appears to be bright.
Mark Shapiro (Cleveland) - Shapiro did a really nice job rebuilding the Indians and turning them into what looks like they will be perennial contenders. They've got a nice, young nucleus that is mostly locked up, and should be mainstays near the top of the AL Central for years.
Omar Minaya (New York Mets) - I personally am not a huge fan of his as a GM, but he's done a nice job. He's made some pretty solid FA pickups in New York that got them deep into the postseason last year and back atop the division right now.
Walt Jocketty (St. Louis) - The Cardinals are struggling this year but Jocketty has had a lot of success in past years. Obviously the Cardinals won the World Series last year, and they were mainstays in the playoffs before that.
Another guy to consider is Brian Cashman, but it's just hard to judge him because we don't know how many of the moves are his and how many are George Steinbrenner's. Josh Byrnes from Arizona is another guy that could wind up on this list in another couple of years, as the DBacks have a nice farm system in place.
If pressed, I think I would choose Billy Beane as the top GM, followed (in order) by Terry Ryan, John Schuerholz, Dave Dombrowksi, and Kevin Towers.
But who do you think is the best? Vote and then give me your reasons in the comments. Please.