Charles Fulton

This plugin suppresses features of the Multisite site creation process:
<ul>
<li>It suppresses the welcome email sent to new site administrators on site creation</li>
<li>It cancels the site creation process if the given email does not exist, instead of creating a local user</li>
</ul>
It also flushes rewrite rules on site creation to address https://core.trac.wordpress.org/ticket/20171.
<h3>Privacy</h3>
This plugin neither collects nor stores any personal, private, or identifying information about any user.

Site Creation Utilities

This plugin improves the Multisite site creation process by eliminating undesired features.

Aaron Edwards

Plugin management for WordPress Multisite that supports the native plugins page and the WPMU DEV Pro Sites plugin! Used on thousands of multisite installs across the web. 
Previously known as WPMU Plugin Manager, it uses a backend options page to adjust plugin permissions for all the sites in your network.
<ul>
<li>Select what plugins sites have access to</li>
<li>Choose plugins to Auto-Activate for all new blogs</li>
<li>Mass activate/deactivate a plugin on all sites in your network (Very Handy!)</li>
<li>Assign special plugin access permissions for specific sites in your network</li>
<li>And as Super Admin, you can override all these to activate specific plugins on the sites you choose!</li>
<li>Removes the plugin meta row links (Version, Author, Plugin) and any update messages for blog admins</li>
</ul>
Also, if you use the excellent <a href="https://premium.wpmudev.org/project/pro-sites/" rel="nofollow ugc">Pro Sites plugin from WPMU DEV</a> you will be able to charge for access to certain plugins!
A free plugin by Aaron Edwards of <a href="http://uglyrobot.com/" rel="nofollow ugc">UglyRobot Web Development</a>.
<a href="https://github.com/uglyrobot/multisite-plugin-manager" rel="nofollow ugc">Contribute on GitHub</a>

Multisite Plugin Manager

I haven't had any issues with the functionality of the plugin, but the interface for granting plugin access to individual sites really needs improvement. Right now it's shoved under the "Settings" tab when editing an individual site, but when a site has a lot of options, this can make the page HUGE. The list of plugins should really be in its own "Plugins" tab, much like "Themes".

Plugin works well but interface needs improvement

This plugin helped me a lot when I had to reactivate one plugin on over 100 sites because accidentally I have activated it for the whole Network previously.

Good job!
Air.

Nice help for multisite

The essential plugin for every multisite install! Manage plugin access permissions across your entire multisite network.

Site Creation Utilities vs Multisite Plugin Manager