On some installs, you may want to have the ability to make quick css-only changes to your theme that are applied just to the blog you are on. Or maybe you’d like to give your users this ability, like you can get at wordpress.com. There are a few plugins available to help you do this. These plugins allow you to add styling rules to the existing theme without editing the actual theme files.
ComicPress/CommPress Companion Although originally designed to be used with the ComicPress theme, it works on any theme, on any setup, and it has a color picker. Throughly tested with WPMU, and I highly recommend you check it out.
They all work by hooking into wp_head in the theme’s header.php file, so if it doesn’t appear to work, that may be why. This way, the styles all get rendered regardless of theme, so if users are switching themes frequently, they will need to know this. If you’re using a small handful of carefully selected themes, and just need to make minor color to graphic changes between them to distinguish each blog, then any one of the plugins above are really just invaluable.
Also, I have not checked any of these plugins for security issues, but you definitely have plenty to choose from.