At ITG, we have dozens of themes installed on our WordPress MU site. We use different themes for different types of blogs. We would like to give any site admin managing a particular blog (for example, a professor managing a class blog) some options in selecting a theme for his or her site. The problem is, an admin with 30+ themes to choose from may be too overwhelmed and discouraged from selecting a preferred theme.
To solve this problem, we at ITG wanted to find a way to specify for any given blog a half dozen or so appropriate themes that would be available to the blog admin(s). Making themes available to all blogs on a WPMU installation is straightforward, but making themes available blog by blog is less straightforward. Fortunately, this is nonetheless possible to do through the core admin options (no plugins required!).
WordPress MU allows site-wide admins not only to enable themes site-wide but also to enable for specific blogs themes that are otherwise disabled site-wide. To find these options, go to Site Admin > Blogs > Edit [for the specific blog you want to enable one or more by-default disabled themes on].
The by-default disabled themes will be listed in a panel at the top right. To activate a by-default deactivated theme (or several) for this specific blog, just click the "Active" checkbox next to the name of the theme (or themes) and click "Update Options" below.
So, in order to customize which themes are available blog-by-blog, just turn off all themes site-wide in Site Admin > Themes, then enable the themes you want available for each blog through the procedure just described. Voila!