I guess the problem (not really aproblem, just a head-scratch) I have in doing this is almost all themes I've tried using with WPMU "work" right on install. Wouldn't the modifications depend on what plugins each site would have? And if everyone is including the same plugins, a sidebar editor or widgets for example, then why not have it bundled in with the WPMU distribution?
I've got around sixty themes in my install, mostly from that zip that was floating around these forums. The only mod I could see to them was a line of code added to check for the sidebar editor plugin, and it didn't have the needed se file in each theme either, which I had to add.
I've even added my own themes, which work in 1.5, 2.0 and up in regular WP and the only things I had to modify to any of them were for things like whatever plugins I wanted it to use - something I would have had to do to any theme, on any of my various WPMU or WP installs.
But hey, if what you're really asking is for some modded themes that have the if/else calls for the more popular plugins, then I'm all over it. :D I'm supposed to be cleaning up my site's themes right now. Might as well benefit everyone else too.