Back in the good ole days of 2009 we had a plugin called Plugin Commander that allowed more control over who saw what plugin and could activate it.
With 3.0 that plugin isn't currently supported (although if you're using Supporter, we've got some options for ya) and I've been looking for a simple solution.
Today I found a plugin in the WordPress repository called "Exclude Plugins". While it's not nearly as advanced as Plugin Commander, but it does the basics of allowing you to have plugins in your "plugins" directory and choose which blogs to activate them on. I hadn't seen it before, though its' been out a little over a month. Thought some other members might be interested.
Here's the link:
And a description:
Exclude Plugins will exclude plugins from appearing in plugins menu for normal user in WordPress multisite. This way, some plugins (excluded plugins) will be available only for Super Admins, while other plugins (included plugins) will be available for normal user.