(I know wpmu 2.7 isn't released :)
Plugin Commander only works partly on wpmu 2.7. You can activate etc from Site Admin->Plugin Commander, but site admin doesn't get access to Plugins (/wp-admin/plugins.php).
This hack (should be added to wpmu 2.7 ?) will give site admin access to Plugins (/wp-admin/plugins.php, line 16):
if( !is_site_admin() && $menu_perms[ 'plugins' ] != 1 )
This is only a hack, I'd prefer that the if statement in line 16 where replaced with a hook e.g. "can_access_plugins"
btw, I've patched plugin commander (added Plugins menu for wpmu 2.7), you'll find it at http://www.soderlind.no/code/view/plugin-commander.php (unsupported and it's a temp fix, you use it on your own risk)