Almost all of our JS is in separate JS files, and we try to take as much of an OO approach to our JS as is sensible in such a OO-hamstrung language. We do have separate "class" files (methods, stateful properties etc) and then script files which are used for event handlers when bootstrapping the page (creating said objects, etc).
Our JS inclusions would typically be along these lines:
<script src="/me/adamcameron/someapp/somepackage/SomeClass.js"></script> <script src="/me/adamcameron/someapp/codeThatUsesSomeClass.js"></script>
// codeThatUsesSomeClass.js var obj = new SomeClass(initParam, anotherInitParam); // do stuff with obj