I have recently started working with Wordpress MS (the new WPMU). I have just installed everything and have a few different domains working off of the same Wordpress MS install.
I am using the WordPress MU Domain Mapping plugin to handle different domain names.
Problem I am having is working with permalinks. I would like the URL to display something like this http://blakebullis.me/sample-post/ ... but whenever I change the permalink settings to be more SEO friendly I get a 404 error. The page only works properly when I use the default permalink settings http://blakebullis.me/?page_id=2
Problem has been solved. I used this article to figure it out http://wordpress.org/support/topic/wordpress-mu-domain-mapping-plugin-052-mysteriously-still-not-working
Within my /etc/apache2/sites-available/[domainname] ... I changed the "AllowOverride None" to "AllowOverride All" for my configuration