I minified JS for performance reasons, rather than to obscure the code. Indeed, you can find a large chunk of the code at http://usejquery.com/sites/315

I tend to avoid jQuery plugins because I like doing as much of the code as possible, so I am afraid I can't recommend any plugins. I largely use jQuery as a selector engine (at which it is brilliant), for event binding and for basic animations.

In terms of refactoring messing up your javascript, I have not suffered major problems with that but I can imagine it happening often on big projects involving lots of people.

Thanks for your interest and good luck with your projects.