This is maybe just to share, for someone stuck googling for a quick and dirty solution. However, if you have any suggestions, particularly less dirty but equally quick solutions, I'm all ears.
I wanted to disable all user welcome/signup emails, because I had a plugin doing auto-provisioning after a user logged in through a CAS-like interface. (Particularly, their passwords aren't stored locally in WP, so the email was confusing at best.) I wasn't able to find a quick/easy way to do so. However, this works:
Create a php file in the mu-plugins folder. It need only contain:
function wind_return_false() { return false; }
add_filter( 'wpmu_signup_user_notification', 'wind_return_false', 11, 0 );
add_filter( 'wpmu_welcome_user_notification', 'wind_return_false',11,0);
add_filter( 'wpmu_welcome_notification', 'wind_return_false',11,0);
add_filter( 'wpmu_signup_blog_notification', 'wind_return_false',11,0);
... or, obviously, append this to the end of your own auto-provisioning plugin.
Hope this helps someone. Again, please comment if I'm doing something particularly unwise.