The jar  file is actually a ziped version of
files.Actually a jar file  can be unzipped using the
winzip utility too!!!!

Make sure that your jar file internally contains a lib
directory. In the lib directory place the
activation.jar and also the mail  jar files.

The expanded structure of the jar file should be

somename.jar
|
|
|-----META-INF
|
|-----lib
|
|
|---activation.jar
|
|
|---mail.jar
|
|
|---pop3.jar (etc)

One thing you can do is unjar the javamail  api, and
again package em up, in your final application  jar
file.
But checkout licensing issues.

Second one is place the mail.jar and activation.jar in
the lib folder and use some kind of installshield to
install your application.

There is a posibility of remotely downloading the jar
files, i,e. java  extension framework.