In my opinion the best structure of packaging your application is:

your-app/
  |---------- bin/           // contains launcher such as a .BAT or
shell script
  |---------- lib/            // contains all JAR libraries related to
your application
               |---------- myApp.jar       // the JAR containing the
main class of ur app
  |---------- docs/        // the JavaDocs pages containing
documentation
  |---------- src/          // the source code of ur app if ur open
sourcing ur app
  |---------- license.txt
  |---------- readme.txt

Hope it helps!

I suggest following the pattern of a Sun JDK as closely as makes sense for your
implementation.  Even going as far as emulating the JDK/JRE distinction.  The
point is that everyone (who knows how to navigate a JDK at all) will be
familiar
with the Sun layout, so they (and any tools they use) will adapt most easily to
your stuff if it follows the established pattern.

(Which, btw, would imply the use of zip files in preference to tar or tgz
archives -- that may be going too far for you, though ;-)

   -- chris