Plugin Management is far superior to Plugin Commander for WordPress MU and multi-site installs. The problem is, Plugin Management was not WordPress 3 compatible. Until this update.
The Problem
I was working on a client site running WP3 with a plugin that allowed PHP to be accepted in text widgets. That is a significant security hole, and it should only be available to the super admin. With WP3 and Plugin Commander, you cannot disable it from the plugin menu. A sub-blog administrator can simply go to the plugins menu and activate the PHP widget plugin.
Plugin Management solves this by letting you control exactly which plugins sub-blog admins can enable. My users could activate Facebook Connect, NextGen Gallery, or Twitter Connect, but not PHP widget plugins or anything else I flagged as restricted. The WPMU team had not updated Plugin Management for WP3, so I did it myself.
The fix was straightforward. In WP3, wpmu-admin.php was replaced with ms-admin.php. A few minor corrections to the PHP and it works.
Installation
Drop mp-plugin-manager.php into /wp-content/mu-plugins/.
Requires WP3+. Use the older version for anything below WordPress 3.0.