organizing JS file in a web application

In any web based JEE application using MVC framework, you will always have 2 sets of JS files along with the standard JQuery framework js files. These are common.js which has functions common for all pages in the application and custom.js which has functions specific to some pages only. In most of the applications I have seen the developers have created only a single JS file having both the custom and the common code which is then included in the header.jsp.

What is the best approach in this case to organize these JS files and are there any best practices?

Thanks

Ashish