I use IntelliJ IDEA, so I don't know about Oracle JDeveloper, and also I use LWJGL, so I don't know about Java3d.
However, when I'm adding libraries and such to my IntelliJ projects, I add them to a lib/ directory in my project directory, and add the libaries to a list of 'project libraries' in IntelliJ. This is how I imagine most Java IDEs would work. I'm not sure that you're guaranteed that your IDE looks in its JDK folder for new things.
I'd also like to recommend IntelliJ IDEA, it's one of the best IDEs I've ever used for anything.