There is a post
here[
^] which describes a solution for master pages and style sheets. JavaScript could be the same solution and using this would make the JS available to all content pages.
If you're wanting the JS
just on the content page, make sure you put it inside the ContentPlaceholder container, right before your closing tag. You won't need to modify your Site.Master if you take this approach.
If you're still having trouble, make sure you try a good Shift+Refresh (F5)
on the page as you might just be seeing the cached copy.
Cheers.