I want to build a very configurable web app where a user can just right-click and add/delete menus.
So I would like to get some suggestions( web links, books, frameworks) that can get me going - from design to development.
I'm willing to using Javascript and/or Java/JSP.

To develop such a system takes years of learning not only the languages and tools but basic design skills. That is, you design in your head on paper what you want the system to do and look like.

It's your design so no one here may do that step. Also, it's odd to call out right click. That's sort of a PC thing. If you want a full on GUI make a web site without coding, I might stick to click and drag then drop since we want to include the Apple gang.

Along the way you'll likely want to have your own web server farm to get early control of the backup that runs this service. That alone may take some thinking time since later you may want to host it on some cloud web service hosting system.