Will Middlebrooks was the obvious choice. Considered by many to be the top prospect in the system, Middlebrooks would have been snatched up by any number of teams if they had been given the chance.
For Lin and Britton, the decision wasn't quite so clear. Any team that takes on Britton would need to have him--a pitcher who gave up a 6.91 ERA in Salem just last year--on their active roster for the whole season. Of course, it's possible a non-contender could sacrifice a roster spot to pick up a guy who was as highly rated before 2011 as Britton was. Lin would not need such a situation, since with his speed and defense he could play a role on any number of teams.
The other side of things are the players who were not added, and now will be eligible for the draft.
I looked at the situation back before the trade deadline, coming up with the following names:
Of those, Chiang, Federowicz, and Fife are all gone in the Erik Bedard trade, and Jason Rice went to Oakland (and then Cleveland) for Conor Jackson. Meanwhile, Lavarnway, Lin, Britton, and Middlebrooks have all made their way onto the 40-man. That leaves Cesar Cabral, Manny Rivera, Jason Rice, and Reynaldo Rodriguez unprotected.
Cesar Cabral has already had the distinction of being taken in the Rule 5 draft, going over to the Rays for a quick try-out in spring training before returning to the Red Sox. He had a solid season in Double-A this year, with a 3.52 ERA and a 46:16 K:BB ratio, so it wouldn't be terribly surprising to see a team take another shot with him--perhaps even the Rays again.
Reynaldo Rodriguez hasn't really done anything above Salem yet, and at 25 years old he's already lagging behind. In the unlikely situation that a team takes a shot on him, expect Reynaldo to be returned before the season starts.
Then there's Manny Rivera, who is to me the most interesting case. He's never had the same hype as Drake Britton, and for good reason, but the lefty has followed a fairly similar career path including the down year in 2011, and has had some amazing peripherals in his time with the team. I don't expect anyone will take him--Britton himself was a bit of a long shot to begin with--but he's worth keeping an eye on, and I think is the only guy on the list that teams might kick themselves for passing up on down the line.
The Rule 5 draft will be held on December 8.