How do I package a JavaMail application into a single jar file along with the mail.jar and activation.jar?

You need to unjar all the JAR files into a single directory tree and then JAR them back up. The trick is preserving the location of some files:

   425 Fri Dec 01 00:05:16 EST 2000 META-INF/javamail.default.providers
    12 Fri Dec 01 00:05:16 EST 2000 META-INF/javamail.default.address.map
  1124 Fri Dec 01 00:05:16 EST 2000 META-INF/javamail.charset.map
   469 Fri Dec 01 00:05:16 EST 2000 META-INF/mailcap