I am just curious, where do I put jar files that are necessary for the program to run, but that a user wouldn't have on their own system? I am using tomcat to run the server. I have three "java" programs. I have one that runs on the server, "connectmanager", one that loads in the browser window for the user, "sessionclient" and the web page one that authenticates a user through MySQL. I need to make sure the user has access to jndi.jar because it is necessary if they choose to upload a picture from their machine.
For easy manageability they're generally put in the same directory as the other applet resources (HTML/JSP page, jar file, images etc.).
If you have several applets that all use the same jar files it would be better to put them in a single, shared directory somewhere in the public web space.