Ellsbury was the best move of all, no one could have predicted that he would become pedestrian with the Yankees. But I'd say Papelbon wasn't a great move if it wasn't for getting really lucky with Koji. I'd say it worked out, but wasn't a "move on from a star who falls off a cliff" with Papelbon.
Bay was a no-brainer, I don't think anyone felt good about his knee situation. Agon and CC were different situations with them just sucking. I don't blame the FO for the trade and signing though as no one saw CC becoming useless and Agon becoming a major problem and his power disappearing.
I completely disagree with OCab. They went from OCab to Rent-an-error, AGon, and then Lugo. From 2005-2008 OCab posted WAR of 2.0+ every year, including 4.2 in '07. In contrast, no one on the RS came even close to posting a 2.0 WAR year at SS. SS was an absolute disaster after 0Cab left. Disaster. It was a terrible decision to let him go, not a good one!
My point was more aimed at what the FO has done since Theo left, not during Theo's tenure (though Beltre technically was at the end of Theo's tenure). Lester/Price, Panda, Lackey trade for Craig/Kelly, Castillo, Cespedes, Ramirez, the whole Bobby V disaster. While Theo made some mistakes of course and the Sox have made good trades/signings since he left, I feel like there are way more boneheaded trades and crazy contracts since he left.