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.

chriscarvache

Enhanced Header / Footer Injections allows you to insert HTML code into the header and footer sections of your templates on a page per page basis. This also works with custom post types, archive pages, the 404 page, the main blog page and the front page (if used). The plugin is designed to help speed up the development process when creating custom sites for clients.

Enhanced Header / Footer Injections

Add code to the header and footer sections of your site on a page-per-page basis.

Multisite wp_head Code vs Enhanced Header / Footer Injections