http://gambolio.com/#/library/
The ui and animations were done entirely using Javascript (with help from jQuery), HTML and CSS. The actual games are flash but the ui is all done using standard web technology.
I do a lot of jQuery as well but have been frustrated lately by how it's simplicity sometimes also makes it hard to maintain. For example as your app grows, you'll inevitably run into problems where your selectors no longer work because of refactoring and etc... Have you faced the same challenges? If not, what do you do to keep down the complexity?
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.