Here are some problems I ran into when setting up Wordpress 3.0 with multiple different domains, along with how I solved them. I figured it's better to get them out on the blog now, and update this post if/when I have more solutions.

Problem 1: I can't load page URLs except when using ?p=xyz permalinks

If you are having problems with page URLs not working on multisite domains, make sure you have: 
    AllowOverride FileInfo Options
defined in your httpd.conf for the directory the Virtual host is in.

Problem 2: The new themes I installed and activated on the main WP 3.0 site do not show up on separate domains

The permissions for separate domains do not get automatically updated when you activate themes on the main site. In MySQL, copy the value for "allowedthemes" in the wp_sitemeta table. This will enable themes on separate domains. Example: 
INSERT INTO wordpress_database.wp_sitemeta (meta_id, site_id, meta_key, meta_value) VALUES (NULL, '2', 'allowedthemes', 'a:2:{s:9:"it-oikeus";b:1;s:9:"twentyten";b:1;}');
where the site_id is the site ID for the separate domain, and meta_value is copied from the first site.

Problem 3: I cannot access Plugins on separate domains

In MySQL, copy the value for "menu_items" in the wp_sitemeta table. This will enable plugins on separate domains. Example: 
INSERT INTO wordpress_database.wp_sitemeta (meta_id, site_id, meta_key, meta_value) VALUES (NULL, '2', 'menu_items', 'a:1:{s:7:"plugins";s:1:"1";}');
where the site_id is the site ID for the separate domain, and menu_items is copied from the first site.

Problem 4: New users are not visible on separate domains

in wp_usermeta, set: wp_2_capabilities = a:1:{s:13:"administrator";s:1:"1";} wp_2_user_level = 10

(NEW June/2010) Problem 5: Upload files not working on separate domains

Replace site_id (2) with your site id in the query below:

INSERT INTO `wordpress_database`.`wp_sitemeta` (`meta_id`, `site_id`, `meta_key`, `meta_value`) VALUES (NULL, '2', 'upload_filetypes', 'jpg jpeg png gif midi mid aac ac3 aif aiff m3a m4a m4b mka mp1 mp2 mp3 ogg oga ram wav wma asf avi divx dv flv m4v mkv mov mp4 mpeg mpg mpv ogm ogv qt rm vob wmv doc docx docm dotm odt pages pdf rtf wp wpd numbers ods xls xlsx xlsb xlsm key ppt pptx pptm odp swf asc csv tsv txt bz2 cab dmg gz rar sea sit sqx tar tgz zip css htm html php js
');

Comments

Kris: Hey Mixu, thanks bro for the tip for allowing new install of wp theme for wpmu, i was looking everywhere, and while i was looking thru the db tables i saw the site meta field and then found your post, THANKS BRO!

John: Thanks for sharing. I was searching for the 'plugins' submenu all over :-)

webber: Great post! After a couple of hours of trying to get it to work, I found your fix and is now working perfect