Any file in this directory with the following filename format will be loaded globally on every page of your shop:
jscript_{unique_name}.js
(where {unique_name} can be anything you want)
Effectively, the file will be loaded as if you had inserted the following into an HTML page:
<script language="javascript" src="includes/templates/{template_directory}/jscript/jscript_{unique_name}.js"></script>