WordPressMU treats plugins a little differently than standalone wordpress does. Namely it supports two types of plugins. Those loaded and controlled on a per-blog basis (like normal WordPress) which are stored in the wp-content/plugins directory; and those that are loaded for all blogs on all pages, which are stored in the wp-content/mu-plugins directory.
I won’t attempt to explain all the good reasons for why these plugins are segregated, instead this is a quick description of a small feature enhancement to the mu-plugins behavior. Namely, one of the differences between how plugins are loaded from mu-plugins vs. how they are loaded in standalone wordpress or the plugins directory; is that mu-plugins only loads php files in the root directory. (It also happens to include all php files, which is another important difference.)
What if you wanted to cleanup your mu-plugins directory a little and store some plugins in subdirectories. Well, here is a simple mu-only plugin that adds this feature.
Install: Rename this file as .php and place it in your “wp-content/mu-plugins” directory.
Usage: You can now place mu-plugins into subdirectories of you “wp-content/mu-plugins” directory and they will load like any other mu-plugin.