Here are some reasons:
In favor of JAR:
- Simple to build and deploy.
- Embedded servers like Jetty are easy to operate.
- Applications are easy for users to start and they can run on their personal computers too, because they are lightweight.
- Starting and stopping applications will require less knowledge than managing web servers.
In favor of WAR or EAR:
- The server would provide features like deployment, restart, security and so on for multiple web applications simultaneously.
- Perhaps a separate deployment team can handle the starting and stopping of apps.
- If your supervisors like to follow rules, they will be happy to find that you are not breaking them.
Having said this, you can always provide 2 or 3 types of executables to cater to all needs. Any build tool makes this easy.