One possible naming convention is to use something similar to the naming scheme jQuery uses. It’s not universally adopted but it is pretty common.
product-name.plugin-ver.sion.filetype.js
where the product-name + plugin pair can also represent a namespace and a module. The version and filetype are usually optional.
filetype can be something relative to how the content of the file is. Often seen are:
minfor minified filescustomfor custom built or modified files
Examples:
jquery-1.4.2.min.jsjquery.plugin-0.1.jsmyapp.invoice.js