I am about to press the "upgrade" button in my Wordpress MU 2.8 install.
What is going to happen to the mu-plugins folder? And is there an equivalent way for me to automatically activate a plugin across all my sites?
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WordPress 3 uses the mu-plugins folder in exactly the same way as MU used to use it. Everything in there is automatically active sitewide.
Note that WP 3 has some newer methods for dealing with plugins though that you may want to consider switching to. For example, the Network Activation allows you to install a plugin via the normal means and then activate it sitewide and still use the WP upgrade system to keep it up to date. The mu-plugins method doesn't allow that sort of thing.