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.

Andy Whalen

WP Hooks is a plugin for WordPress that allows you to add JavaScript, HTML, or other code to your 
header and footer without modifying your theme. WP Hooks uses the wp_head() and wp_footer() hooks 
built in to WordPress to add content to your header and/or footer. It’s great for those who have 
custom JavaScript, CSS, or other code (Google Analytics, meta tags, etc.) in their header or footer 
and don’t want to or can’t modify their theme.
Find <a href="http://amwhalen.com/blog/projects/wp-hooks/" rel="nofollow ugc">more instructions and discussion</a> on the WP Hooks home page.

WP Hooks

WP Hooks allows you to add JavaScript, CSS, meta tags, etc. to your header and footer without modifying your theme.

Multisite wp_head Code vs WP Hooks