Hey guys, I know you'll love this as a lot of you are requesting it around here.
After getting the Supporter plugin, I took a day to create a new plugin managment plugin that supports the native WPMU plugins page and the WPMUdev Premium Supporter plugin!
This is a rewrite of Plugin Commander and is intended to replace it. It uses a backend site admin options page to adjust plugin permissions. The big difference is that users can activate their plugins on the regular WP plugins page! This is the first plugin of it's kind to use the new hooks added in the WPMU 2.7 plugins page and a little creative genius to allow no hacking of core files. Also, if you use the excellent Supporter plugin from premium.wpmudev.org you will be able to choose which plugins can be accessed by supporters only!
For WPMU 2.7.1+ only! Might work for 2.7, but before that the hooks were not in plugins.php yet.
Check it out: http://wpmudev.org/project/wpmu-plugin-manager