I have made a webpage showing step-by-step how to configure NVIDIA's Nsight graphics debugger to work with Java/JOGL. Have a look and let me know if it works for you, or if I've made any mistakes, or if you think it can be improved:
http://ecs.csus.edu/~gordonvs/nsight.htmlIt's incredibly cool to be able to peer inside the shaders while the program is running!