Referencing a javascript file on a site via the masterpage turned out to be a bit more involved than I thought it should be.
I built a web template to roll out a branding feature which included uploading a javascript file into the style library folder. I then wanted to reference the javascript file in the masterpage. Relative URL's are not an option due to the fact that once you start delving into sub folders the links to the javascript file will break. And the alternative, putting in a reference to the sites base url, seemed to be impossible according to the lack of results via google (and bing)...
The solution I finally stumbled upon was to use the script manager tag.

Here is a simple method of how to embed an mp3 file into css and play it in an application.

There is not alot of info out there on how to do this and I found out basically by trial and error so I hope this may be of use to some of you. Also... I'm not sure if this is the best practise way of doing this, there may be another way that is simpler or better... please let me know if you find something