Players are subtracted after the season ends. All players eligible for free agency file on the day they are allowed to. This subtracts free agents off the roster. Usually at the same time, all 60 day DL players are added back to the 40 man roster. And to create space for new players who will be acquired via trade and free agency, teams generally remove players from the 40 man roster that they either no longer want or think are no longer worthy of holding a 40 man roster spot.
Including the eight players the Mets have on the 60 day DL: Johan Santana, Ike Davis, Bobby Parnell, Scott Rice, Jeremy Hefner, Matt Harvey, Jennry Mejia and Josh Edgin, the Mets have a total of 48 players on their current 40 man roster. According to Cot's Baseball Contracts, the Mets have 6 players who are eligible for free agency: Frank Francisco, LaTroy Hawkins, Pedro Feliciano, Daisuke Matsuzaka, Tim Byrdak and David Aardsma. Two players: Johan Santana and Aaron Harang have team options for the 2014 season. Assuming the club options are not picked up for Santana and Harang, that will leave the Mets roster at 40. I am not sure if Carlos Torres qualifies for free agency, so I will assume he does not. If so, that puts the Mets roster at 39.
Next comes the difficult part. It now needs to be determined what players of these remaining 40 should be removed to make room for said new players. I set up two categories: one for players I would remove and another for players that I would keep, but could be removed. I would remove pitchers Sean Henn and Greg Burke, infielders Omar Quintanilla and Jordany Valdespin, outfielders Kirk Nieuwenhuis and Mike Baxter and catcher Anthony Recker. Both Henn and Burke can be brought back on minor league deals. Valdespin has worn out his welcome and Baxter and Nieuwenhuis have not been good enough players to warrant a 40 man spot. Quintanilla is a tough decision because he has been the Mets starting SS. But, I would expect to see the Mets upgrade at that position and it would not make much sense to keep Q as a backup. He provides little value on the bench. Similar to Burke and Henn, the Mets may be able to bring him back with an invitation to spring training. Recker had a couple moments, but he does not warrant a 40 man spot. Once again, the Mets can sign him to a minor league contract if they wish to bring him back next season.
There are a handful of players who the Mets may decide to remove. This includes pitchers Scott Atchison and Robert Carson and OF Andrew Brown. If either of the three were removed, I wouldn't object, but prefer to hold onto them for now. Other possibilities are RHP Torres, LHP Scott Rice, catcher Juan Centeno and infielders Zach Lutz and Wilfredo Tovar. All four help the Mets with depth at their respective positions, so I would not consider removing any of them. I would also hold onto 1B Josh Satin, RHP Hansell Robles and OF Cesar Puello. With the 7 players off the 40, the Mets would go into the offseason with 33 players, with the possibility to get the number to 30 if they choose to cut Atchison, Carson and/ or Brown.