Here’s some of the things you should be doing:
- Testing (especially automatic and functional testing)
- Breaking up code into logically organized files
- Using and organizing client side templates
- Making plugins that clean themselves up are internally organized, and extendable.
- Error reporting
All of these things are hard or impossible to do right with jQuery alone.
You can add your own automated testing library - Selenium or qUnit, qUnit isn’t automated. Selenium is hard to write tests for.
You can add your own documentation engine - JSDoc, but make sure you keep track of every file!
You can add your own way of loading and compressing scripts - RequireJS.
You can use other client side template libraries - jquery-tmpl, but you won’t be able to compress them into your build or put them in external files as easily.
You can be careful to structure your jQuery plugins so they can be easily removed from an element, remove all event handlers, and provide some mechanism for extending or overwriting your plugin.
You can devise your own way of doing error reporting.
js steal/generate/app APPNAME
and get all of these things for free.