Jan Štětina

Includes custom HTML/CSS/JS code in the section on every blog in the network.
Very simple, but sometimes useful plugin.
After activation visit Network Admin –> Settings –> Multisite wp_head Code for setup. Nothing else is needed.
Developed for private use, but has perspective for more extensive usage. I can’t guarantee any support in the future nor further development, but it is to be expected. Kindly inform me about bugs, if you find any, or propose new features: <a href="mailto:zaantar@zaantar.eu?subject=[multisite-wphead-code]" rel="nofollow ugc">zaantar@zaantar.eu</a>.

Multisite wp_head Code

Includes custom HTML/CSS/JS code in the  section on every blog in the network.

jwilsson

WordPress adds all kinds of <code><meta></code>-tags to the <code><head></code> section of your site. 
Some of these tags are quite good and have real uses, others make sense for some sites and others doesn’t. 
Some tags are even considered a security risk, since they tell the world which version of WordPress you’re currently running.
This plugin allows you to remove all of the <code><meta></code>-tags that WordPress outputs by default. 
You decide on a tag-by-tag basis which tags to remove and which to keep. Nothing’s enforced, you’re 100% in charge.

wp_head() cleaner

Great plugin

Remove unused tags from wp_head() output.

Multisite wp_head Code vs wp_head() cleaner