I went through the hassle of talking to two developers who ended up not being able to help me out. I eventually tried to get it set up on my own.
I am running WP3.0 Multisite with Buddypress. I want to basically host my wp-content/themes, wp-content/uploads, and wp-content/blogs.dir on Amazon S3. I have already opened an account.
So far I have tried both W3 Total Cache and TanTan's Amazon S3 plugin, but neither seem to work with multisite. TanTan's doesn't have options to include the blogs.dir folder, and while I can add that functionality under W3 Total Cache, the plugin just gets failed requests when I try and upload my theme folder, despite the site being setting up correctly.
Also, both of these claim to have multisite functionality, but don't seem to. If I put TanTan's plugin in mu-plugins, or activate it sitewide, other users can see it and the settings change per-user (it asks for a different Amazon key rather than saving it). Obviously users shouldn't see that dialogue unless they are site admins, but they do.
Can someone lend me a hand here?