When I first started programming special functionality for WordPress MU I wrote several mu-plugins for the aggregated homepage.
Today in a bright moment I felt I’d better use the functions.php file and add it to the aggregated-theme.
My new convention
A mu-plugin should be a plugin for adding functionality which needs to be available for all, or at least a lot of blogs.
The functions.php file includes functions which are related to a specific blog.
So adding extra functionality to the aggregated-theme should be done by functions.php instead of mu-plugins.