Paolo's general idea (i.e. effectively changing some part of the request uri) is your best bet. However, I'd suggest using a more static value such as a version number that you update when you have changed your script file so that you can still get the performance gains of caching.
So either something like this:
<script src="/my/js/file.js?version=2.1.3" ></script>
or maybe
<script src="/my/js/file.2.1.3.js" ></script>
I prefer the first option because it means you can maintain the one file instead of having to constantly rename it (which for example maintains consistent version history in your source control). Of course either one (as I've described them) would involve updating your include statements each time, so you may want to come up with a dynamic way of doing it, such as replacing a fixed value with a dynamic one every time you deploy (using Ant or whatever).