Recently the Mets Farm System was ranked by ESPN.com while placing 17th.
"It took a few major trades, but their system finally has thinned. Their international scouting department has saved the system, with three of their top six prospects (Fernando Martinez, Wilmer Flores and Jefry Marte) all coming via that route. Keep an eye on Brad Holt, a potentially fast mover from the 2008 draft whose curveball is improving."
Everyone knows about Fernando Martinez as he has been regarded as the Mets top prospect for awhile now but Flores and Marte both have tremendous potential. Both are very young and had very strong season's last year so this upcoming year will be especially important.