WordPress MU

I've got a main site with several cpanel add-on domains in attached subdirectories. So it looks like this:

mainsite.com
othersite.mainsite.com (also accessible through othersite.com)

I'm moving everything over to wpmu, but I'm not sure if having the vhosts wildcard set up will kill my the add-on domains?

It won't if you put your subdomain vhosts above your WPMU vhost that has the wildcard in it. It will read the previous vhosts first and if not, then use the WPMU wildcards.

Trent