How do I add JavaScript that will execute on all my sites in Multisite?

Your answer, Kyle, is the mu_plugins folder. Create it within wp-content. Any php file put in here will be automatically loaded into ALL multisite blogs (or any non-multisite blogs).

This is a great area to put plugins vital to the site working, or shared functionality such as custom post types, taxonomies, filters, etc. Really anything! The main bonus here is when updated said “shared” files, you don’t have to do it in every single theme that utilizes it! It’ll be available for all themes, on all sites.

If you want to sort your stuff within mu_plugins just put everything in a nice folder structure, and create a index.php or load.php in the root of mu_plugins where you can load everything in.

From there, wp_enqueue_script just as you normally would!