Some of the best java applications that I have seen tend to use the tanuki wrapper for this.
It standardises startup scripts across different OS's, i.e. can be used to configure a *nix daemon or a windows service.
It provides a standard command line interface for stopping, starting, restarting and checking the status - running or not.
I appreciate seeing it used more and more, as I don't have to learn it again, learn it once and reuse it again and again.
By using this service library, your application can benefit from future enhancements.