You need to create an appropriate script in /etc/init.d and link it to /etc/rcX.d directories. The script should support at least start, stop, and status parameters. During start it should run java command with appropriate arguments, probably via nohup java &. Then you should save PID of your newly-started process to file /var/run/yourservice.pid. stop command should read this PID file and kill this service.
The details vary from distribution to distribution, most distributions provide some macros to make whole job easier. It's best to look at examples of other services in /etc/init.d for your distribution.
Additionally:
If your service isn't accessed from other computers from the network, but it opens some port, make it unavailable with firewall.
If your service processes some 'delicate' data, it's good to add another user and invoke an appropriate sudo command in your /etc/init.d file.
