To remove unselected compositions and unused footage items from selected compositions in the Project panel, choose File > Reduce Project. This command is available only when the Project panel is active, and removes both unused footage items and all other compositions that are not included within a selected composition as nested (subordinate) compositions.
If the selected composition includes items that are turned off (that is, the Video or Audio switch is deselected in the Timeline panel), the Reduce Project command does not remove those items.
Note: If an expression in a selected composition refers to an element in a nonsubordinate composition, Reduce Project removes the nonsubordinate composition and the applied expression. The message that appears after you choose Reduce Project reminds you of this possibility, so you can undo the command if needed. To avoid removing the expressions from a nonsubordinate composition, drag the nonsubordinate composition into the composition that refers to it. Then deselect the Audio and Video switches for the composition that you added. Thats compliments of AE help.
Oh yeah and you can also use file > remove unused footage.
~Colin