Custom workspace data for After Effects CS3 is stored in:
Same general path for CS4 and CS5, just substitute 9.0 or 10.0 for the version folder. Windows users can find the folder under C:\Users\username\AppData\Roaming\Adobe\After Effects. (Windows XP: C:\Documents and Settings\username\Application Data\Adobe\After Effects\)
The UserWorkspace#.xml files represent the different workspaces you've created. Open the file and inspect the UserName value (at the bottom) if you need to know which workspace it is. Note that if you haven't explicitly given your workspace a name (via the Workspace menu > New Workspace), the UserName value may be a duplicate of the last workspace you were working in. ie., Standard, Animation, etc.