Running a java JAR as a daemon in Linux is fairly easy, but it took me some digging to figure out how. This is using the new upstart init script functionality, which is included in recent distributions of Ubuntu.
Instead of creating a script in /etc/init.d, as with System-V init, you create a .conf file in /etc/init. The syntax is much simpler, and upstart takes care of PID files and killing the process for you. You don't have to mark the file as executable.
This particular example is for a java JAR by SauceLabs for their SauceConnect service. All you have to do is create the following as /etc/init/sauceconnect.conf, where "sauceconnect" is the name of the service you will be invoking with service start/stop.
description "SauceLabs SauceConnect Service" author "Chase Seibert" start on runlevel  stop on shutdown expect fork script cd /home/chase/bullhorn/tools/sauceconnect java -jar /home/chase/bullhorn/tools/sauceconnect/Sauce-Connect.jar USERNAME PASSWORD >/var/log/sauceconnect.log 2>&1 emit sauceconnect_running end script
That's it. Now you can issue the "service sauceconnect start" and "service sauceconnect stop" commands. You can tail /var/log/sauceconnect.log to verify that it's working.