Jeff Sackmann of Brew Crew Ball and columnist for a few other sites has this article on Baseball Analysts today discussing who the best Minor League Defenders were this year.
According to his work, Jayson Nix is a decent defensive 2B, Ian Stewart and Phil Cuadrado are roughly the same defensively per 150 games(though Ian logged more innings) and Troy Tulowitzki needs to improve his D in order to stick at short. But remember Jeff's warning: It's only one complete year of data and he's still working this out.
Update [2006-11-30 21:10:32 by Russ in NY]: The Rockies announced the 24 players who will attend their winter development program. Chaz Roe, Josh Sullivan and Michael McKenry are the most interesting names on that list to me. Yeah, the Rockies are taking it nice and slowly with Frankie Morales during the off-season as well.
Update [2006-12-1 10:24:10 by Rox Girl]:
Today Sackmann put up his "worst defender" lists. Rockies prospects making this dubious distinction include Chris Nelson, Corey Wimberly, Daniel Carte and surprisingly given his reputation, Jeff Salazar. All players' defensive stats are now available at MinorLeagueSplits.com.