You have to reference your executable in
/etc/rc.local file (or add a system startup service
/etc/rc2.d: the Pi boots to runlevel 2).
There, you put a normal
java invocation with full path (i.e.
/usr/local/bin/java ... or
If you want the output to be logged to a file, you either leverage
syslog function or redirect the output to a logfile (or two separate logfiles, one for stdout log, one for error log), i.e.
/path/to/java -JAVA_OPTIONS your.class >> /var/log/logfile.log 2>> /var/log/logfile.err
The first time, run the command from the command line to verify it is properly working.