I am creating a desktop application that uses JOGL. Java webstart technology does a fine job of ensuring a user will have the neccessary JOGL jar files. For my project, a user must be able to start the application outside of a web browser. How can this be accomplished?
Simple: learn how to package jar files with your own application. The basic gist of it is that in your executable jar you will need to add a manifest file with a class-path line that defines all the libraries that must be on the classpath of the application. IDEs like Netbeans and Eclipse can automate this task for you.
[link to documentation|http://java.sun.com/docs/books/tutorial/deployment/jar/]
Is it common practice to package jogl.all.jar, nativewindow.all.jar, and newt.all.jar with a desktop application that uses JOGL? Should I package gluegen-rt.jar as well? Is this how applications are deployed that use java extensions?
it is common practice to package all jars that you actually need to be able to run the application. I don't know which ones your application specifically needs, I would think you would know this yourself since you need the libraries also when compiling it.