Ozh’s Theme Toolkit allows theme authors to easily incorporate an admin menu in their themes to facilitate user customisation. It does not work too well out of the box with Wordpress MU, displaying some undesirable behaviour like the menus persisting to appear despite the user having chosen another theme. This version has been modified to work with Wordpress MU and has been tested on the r542 nightly.
Simply replace the existing themetoolkit.php with the one in the archive in all your themes (or use symbolic links if you want).
Do let me know whether it works for you or not!