After the Nomar trade:
3b went from Mueller to Lowell (good call)
1b went from Millar to Youk (good call)
SS went from OCab to miscellaneoud (OCab became a journeyman so it's not a big loss)
2b went from Bellhorn to Pedroia (remains to be seen if this was a good idea)
LF stayed with Manny until 2008 when Manny forced his way out of town (can't blame Theo here)
CF went from Johnny Damon to Coco Crisp/TEllsbury (good call)
RF went from Trot to JD Drew (good call)
C stayed with Tek until 2011
He dumped Pedro and Lowe when other GM's may have kept them on for nostalgia. He found a suitable replacement at closer.
Theo kept trying to bring in high priced talent while consistently adding young talent from the farm system. I really can't fault Theo for much of anything from 2005 - 2011. He should probably still be the GM today, but LL had JH's ear and they dumped the wrong guy.