Marcus (aka @msykes)

=THIS PLUGIN IS ONLY USEFUL IF YOU’RE USING MULTI-SITE MODE=
This is the same plugin previously available at <a href="http://firestats.cc/wiki/WPMUPluginCommander" rel="nofollow ugc">http://firestats.cc/wiki/WPMUPluginCommander</a>, which has been used reliably with wordpress multi-site networks for many years.
Plugin Commander is a plugin management plugin for multi-site mode, which allows further control on network-activated plugins.
It allow you to do the following things:
<ul>
<li>Mark any plugin in the plugins directory to be automatically activated for new blogs.</li>
<li>Mass activate or deactivate a plugin for all existing blogs</li>
<li>Choose which plugins users can activate and deactivate through Manage->Plugins, for this to make sense you need to disable the built-in plugins menu (through Site Admin->Options->Menus)</li>
<li>Activate and deactivate plugins for specific blogs, even if the blog owner is not allowed to control those plugins.</li>
</ul>

Plugin Commander

Plugin Commander is a plugin management plugin for multi-site mode, which allows further control on network-activated plugins.

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.

Plugin Commander vs Multisite Themes