Jhonny Peralta 2012: 585 PA, .239/.305/.384, 13 HR, 2.5 WAR, $5.5 million salary
Jhonny Peralta 2013: 436 PA, .305/.361/.461, 11 HR, 3.7 WAR, $6.0 million salary
Nelson Cruz 2012: 642 PA, .260/.319/.460, 24 HR, 1.1 WAR, $6.25 million salary
Nelson Cruz 2013: 452 PA, .269/.330/.511, 27 HR, 1.5 WAR, $10.75 million salary
Aside from Ryan Braun and Alex Rodriguez, the two biggest names involved in the Biogenesis suspensions are both up for free agency after this season.
If not for the PEDs revelation, they'd both be headed toward massive pay days. Even though they only played for roughly two-thirds of the season, they each had a WAR that was at least 35 percent better than 2012.
Instead, they'll probably now be viewed as liabilities in their early 30s who either might not play as well without PEDs or might get busted a second time for trying to cheat the system.
The fly in this theory's ointment is that Melky Cabrera was suspended for the final 45 games of the 2012 season and still ended up signing a two-year, $16 million contract with the Blue Jays. If a team thinks either Cruz or Peralta is worth signing, it doesn't seem likely that they'll let the final two months of this season impact that decision.
However, Cabrera has played pretty terribly this year, putting up numbers not much unlike those he posted in 2010 with the Braves—arguably the last time he was clean, considering his huge spike in production the following season. Teams may at least be skeptical about how much return they can expect on such an investment.
Not only is the fallout of Biogenesis likely going to affect their value on the open market, but how they're paid this offseason could legitimately impact the future of performance enhancing drugs in baseball.
If Cruz and Peralta still get their millions, would the threat of a 50-game suspension really keep up-and-coming players from doing whatever it takes to get ahead? If they are instead effectively boycotted and only able to make a small fraction of their previous salaries, perhaps that would be more of a deterrent for the future.