Please see Replace Your Preferences for the paths to both the InDesign Defaults and InDesign SavedData files (the only two files you need to move to match your prefs). Custom keyboard shortcuts and workspaces are both saved in subfolders of the directory where InDesign Defaults is stored. Moving workspaces has been reliable for me, but be careful about moving shortcut sets. CS4 shortcuts are not compatible with later versions without running a script (John Hawkinson wrote one to do this, but I don't seem to have a link). I don't know if CS5 and 5.5 shortcuts will work in CS6. Symptoms of a problem are keys that no longer work as expected, and perhaps crashing.
In that link you'll also find information on backing up and moving other presets.