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.

Yuki Sugitani

This plugin allows you to organize the contents of the head tag that WordPress automatically outputs. 
You can use the checkboxes to choose which tags to remove.

Tidy Head Tag

This plugin allows you to organize the contents of the head tag that WordPress automatically outputs.

Multisite wp_head Code vs Tidy Head Tag