The biggest problem is that the default archiver may open your JAR instead of letting Java run it.
There are several solutions to package JOGL projects:
- applets (they won't work when NPAPI stops being supported in the web browsers, they're dying, JDT is already blacklisted and you have the same constraint than Java Webstart for the certificate)
- Java Webstart / Icedtea Webstart (fast, simple but now you have to buy a "trusted" certificate, Oracle often modifies its security requirements which drives it very difficult to run anything without getting tons of warnings and you need to do something under Mac to allow applications from Internet)
- self-contained applications with native installers (you need a different native installer per OS, you can bundle the JRE with your application)
- other cross-platform installers: IzPack, GetDown, ...