Multisite javascript – where's the right place?

Where is the right place to install JavaScript to affect all sites on a multisite setup? Based on other docs I read, you’re supposed to put JavaScript into wp-content/themes/name-of-your-theme/*.js and reference it from functions.php. But this is bad for several reasons:

• It affects only 1 theme, and in multisite, there may be many themes active.
• Updating the theme may overwrite the functions.php file, losing your changes.

So what is the right approach? Some examples of what I’m trying to do with JavaScript:

• On wp-admin/post-new.php, require the new post to have a non-blank title
• Add and hide some gadgets on wp-admin/user-new.php

Thank you.