Adding custom javascript

I wanted to extend my markdown preview with a simple javascript function.

Adding tags does not work because javascript cannot be loaded after the page loads. Unless you use eval() **Shutters**

I tried finding or creating a hook in the source file, but I am not sure where to look. (my best guess currently is somewhere in app/pages)

I was wondering it there is a better way of doing this. Perhaps this could be an official feature.