I usually only like implementing JavaScript if it will add functionality to a webpage. It keeps the application running its best and performing optimally. It’s one of the same principles that I suggest with regards to using Flash as well.

With that being said I’ve seen lots of great Flash graphics/animations and creative uses for JavaScript for styling a page. DevSnippets has a list of 20 plugins based on jQuery for adding style to design elements.

I would probably say implementing some of these into your next web application will give it a clean look, but don’t overdo it. If it’s something that could be handled in CSS I would make an attempt there first, then look into JavaScript.