I would really like to see a way to make posts only readable by registered blog users. This would be something like the nifty Viewlevel plugin, but for obvious reasons, that won't work with WP2 or WPMU.
I don't have the coding saavy to do this, but this problem prevented me from using WPMU for a hosting project of mine.
This should also be very useful as a plugin to WP2. For WPMU, it might be nice to let subscribers, contributors... or whatever of other blogs hosted on the same server to read...