Baseball America has compiled a lengthy list of minor league free agents. You can view their full list here.
Players from the Mets organization who are now free to sign anywhere are right-handers Yhency Brazoban, Brian Bruney, Chad Cordero, Jack Egbert, Johan Figuereo and Carlos Muniz; left-handers Derrick Ellison, Arturo Lopez, Mike O'Connor, Adam Pettyjohn and Raul Valdes; catchers Michael Barrett, J.R. House, Salomon Manriquez and Luke Montz; first baseman Marshall Hubbard; second basemen Russ Adams, Alex Cintron and Jonathan Malo; third baseman Mike Cervenak; shortstop Jose Coronado; and outfielders Brahiam Maldonado, Jorge Padilla and Jesus Feliciano.
UPDATE: Add Mike Hessman and Omir Santos to the list. Both were outrighted and opted for free agency.