After a couple more weeks of experience with PluginCommander for WordPress MU, its limitations are becoming clearer. To be specific, some WP plugins just don’t like it; they’ll throw a fit when attempting to activate them via PC, dumping a seeming endless array of errors on the page.
So while I’m still using PC for those plugins that can be reliably auto-activated during blog creation, I’ve turned to Plugin Filter when giving individual users access to potentially problematic or premium plugins. PF allows me to turn back on the stock Dashboard Plugins menu (which, let’s face it, is a smoother experience than the PC replacement) while still restricting users to activating a limited set of safe plugins.
To make PF work, just drop it into mu-plugins, and then open each of your restricted plugins in a text editor. Look for the line that reads something like:
Plugin Name: My Random Plugin
…and change it to:
Plugin Name: My Random Plugin: SiteAdminOnly
From that point on, only the site admin (you) will be able to (de)activate that plugin. Of course, every time you upgrade the file(s) in question, you’ll need to make this change… but it’s a relatively simple tweak that takes just a few seconds.