To figure the overall top three, it's simply a matter of assigning three point for a third-place score, two for second and one for third. Really easy stuff. So here we go:
2005: 3. Jason Varitek 2. Manny Ramirez 1. David Ortiz
2006: 3. Jonathan Papelbon 2. Manny Ramirez 1. David Ortiz
2007: 3. Mike Lowell 2. Jonathan Papelbon 1. Josh Beckett
2008: 3. Jon Lester 2. Kevin Youkilis 1. Dustin Pedroia
2009: 3. Jacoby Ellsbury 2. Jon Lester 1. Jason Bay
There may be some controversy here. No Manny or Ortiz after 2006 could be debated. But I think that these choices are definitely defensible.
Going with these choices, that would make the following players the three best players for the Sox between 2000-2009:
3. David Ortiz: In his seven years in Boston, Big Papi has hit 259 home runs and is hitting .288 with a .967 OPS (OPS+ 145). He has 830 RBI and 1065 hits. He currently ranks sixth in homers, fourth in OPS and seventh in RBI all-time in Boston history. He is widely considered one of the most clutch hitters in Red Sox history and was a key to Boston winning their first title since 1918. Despite his off-season in 2009, over the last seven years in Boston Ortiz has become one of the most feared designated hitters in the AL.
2. Pedro Martinez: In the first half of the decade, Pedro led the AL in win percentage twice, ERA three times, WHIP three times (including the lowest mark of the modern era with .737 in 2000), and strikeouts twice. He was The Sporting News Pitcher of the Year in 2000, won the Cy Young in 2000 and finished in the Top Four 2002-04. He is one of the best pitchers in Boston's history and was the most feared pitcher in the AL during his time with the Sox. If you were fortunate enough to see him pitch in person, you saw greatness.
1. Manny Ramirez: You could easily make the argument that Manny Ramirez is the best right-handed hitter in Boston's history*. A combination of power and average, Manny was a constant threat every single time he stepped to the plate. And he did it all with such ease that he almost looked lazy as he did it.
In eight years in Boston, Manny hit .312 with a .999 OPS (OPS+ 155). He had 274 homers, 868 RBI and 1232 hits. He went to seven straight All-Star games and was the World Series MVP in 2004. Between 2001 and 2006, Manny never had less that 33 homers, 100 RBI and 140 hits. He was the one constant in a lineup that saw massive change over his eight years in Boston; Manny was the only player still in the starting lineup in 2008 that was there in 2001. But will he be remembered for all this, or for the "Manny being Manny" stories? The PED suspension that came after his tenure in Boston? That's the question.
* The only other real choice here is Jimmy Foxx. That's not a dig on Dewey, Doerr or Rice. It's just the reality; from the right side of the plate it's Manny, Jimmy and everyone else.