Maxaud

(NOTE: Before saying this plugin is broken, please understand what this plugin does. It’s meant for WordPress installs that have multiple NETWORKS.)
Adds the ability to have different themes available to different NETWORKS in a multisite atmoshpere.
WordPress allows for multiple “networks”, these are not to be confused with sites. A network holds blogs underneath of it.
This plugin will allow you to separate themes into different directories so they’re only accessable and viewable to the networks you choose.
The plugin will attempt to create a directory in the /wp-content/ directory named /ms-themes/. If it fails to create it, then you will need to make one.
In the /ms-themes/ directory you will create a folder for each network that you want to allow only certain themes to.
Example: 
If you have a theme named “Snarfer Theme”, and you want to only allow it to be viewable/available to the network (and all sites on that network) with the site_id of 7, you would place the snarfer theme directory in /wp-content/ms-themes/7/
Future releases:
<ul>
<li>Network option to turn off auto creation on/off network directories, index.php files.</li>
<li>Network option to display network ID in the footer of sites so network admins can easily tell what network a site is under.</li>
</ul>

Multisite Themes

Adds the ability to have different themes available to different NETWORKS in a multisite atmoshpere.

hazardcell

A newer version for WP3.0 is in the works. I would have loved to release it on time for the release of 3.0 but I’m having my finals at the moment so it will have to wait until June 2010. Will include single sign-on as well.
This plugin is for WordPress MU
This plugin basically allows you to host blogs on multiple domain names while maintaining one main site.
For example, the main site could be example.com but users will also be able to sign up for blogs on example.net, example.org or any other domain name that you choose to add.
<ul>
<li>All the sites will have the same settings</li>
<li>No extra blogs/tables are created for the additional domain names</li>
<li>All blogs will be viewable on the Site Admin blog list</li>
</ul>
Alternatively, if you would like to request a feature and/or report a bug, please visit the <a href="https://wordpress.org/tags/yet-another-multi-site-manager" rel="ugc">forum</a> or the <a href="https://plugins.trac.wordpress.org/browser/yet-another-multi-site-manager/" rel="nofollow ugc">trac repository</a>. You will have to login with your WordPress.org username and password to access these.
<h3>Known Issues/Limitations</h3>
<ul>
<li>Remote login does not work with this version</li>
<li>Only tested with VHOST installs in root directory</li>
</ul>

Yet Another Multi-Site Manager

Allows blogs to be created on multiple domain names while maintaining only one main site for all domain names.

Multisite Themes vs Yet Another Multi-Site Manager