I've recently been using jQuery. I've found it generally easier to use than Prototype. The documentation is also very good.

I was looking for a plugin that would allow me to do lists of files. I found this great jQuery plugin called Tree Table Plugin which also supports drag and drop.

It looks really good and has some useful advanced features, such as good integration with AJAX.

Another plugin I found which looks good is for augmenting textareas called markItUp!

This is a very polished looking textarea editor tool, which supports various different kinds of markup languages.