There are a couple of obvious answers.
Middle Infield - The signing of Mark Grudzielanek on Sunday wasn't a bad one, but I think it's fair to say that a lof of people were hoping for a bigger splash. In spite of the depth Grudz can provide, is this still the team's biggest weakness?
Bullpen - There have been some gutsy performances from some unlikely places this season; Jose Mijares and Bobby Keppel have been pleasant surprises, R.A. Dickey has played his role and Matt Guerrier has rebounded after a rough time last summer. But there's always room for one more firefighter. At this point would you rather have a guy like Scott Downs? (Downs, by the way, was dealt to the Twins by the Cubs in late '98; six months later he was shipped back with Rick Aguilera, while Chicago sent us Jason Ryan and somebody named Kyle Lohse.)
Rotation - No denying the talent available for the price they're being paid, but some stability and dependability would be great. This doesn't have to be Roy Halladay here, just a proven commodity, tha'ts all we're asking for.
Bench Depth - Mike Redmond, Brian Buscher, Brendan Harris and Delmon Young don't give this club enough offensive depth. Bringing in someone who can pinch hit just somewhere, anywhere in the bottom half of the order would provide an invaluable service to a team that struggles with production at the bottom.