How Do I Package and Deploy an Eclipse Java Application?

Have a look at the Fat Jar Plug-In.

That's because desktop deployment isn't well defined.

You are heading into release issues which is a huge can of worms.

I assume you have some form of version control like SVN or git? If so check out maven with the release plugin and maven-assembly-plugin

It'll take a lot of work to setup, but once you get it going you'll be cross linking and deploying distribution packages in no time!

Plus you'll have access to the vast maven repos on the web right now