I am still confused. The jar file I mentioned is an java application. I have the image file, but I don't know how to make it a logo for my application. Should I put it into the manifest file somewhere or what? Thanks!
Well it depends on the OS you are using, but if its Windows you can't control what icon is used with a Jar in the Jar itself. The icon to file type relationship is maintained by Windows, so you would have to change it there.