With Maya 2011, you will see there is a new retargetting system called HumanIK (or HIK) . This is a great system and I would certainly recommend using it, but for those of with a pipeline using FBIK you will notice the tools that were under Skeleton -> Retargetting seem to be gone....
no fear, although the UI does not show the tools they are still accessible through MEL. You need to copy and paste these commands in the Script Editor windows and type in the commands italics
Skeleton -> Retargetting -> Set Target Neutral Pose is setRetargetRestPose;
Skeleton -> Retargetting -> Go to Neutral Pose is assumeRetargetRestPose;
Skeleton ->Retargetting -> Retarget Skeleton (option box) is RetargetCharacterOptions;