I have setup SabNzbd, Couchpatato, Headphones and Sickbeard on 2 freenas boxes 2 different ways. One where all the apps, python etc is on a zfs volume and run as a service on FreeNAS and the other setup used the Serviio Jail example found here
http://forums.freenas.org/showthread.php?1399-HOWTO-Install-Serviio-in-Freenas-8-0-x and i just installed the extra apps into the jail.
It took more work to get the jail setup initially but it was by far the best setup option for the following reasons.
1. Makes it very easy to app new apps without changing Freenas or its config at all
2. Upgrades to Fressnas are much easier as you just need to run a simple script to re-enable the jail after you upgrade. If you install everything directly in freenas you need to make any change you made to the main filesystem again on upgrade which is a real pain.
3. Anything you install in the jail does not break the Freenas system. (I broke freenas at one stage when not using the jail by doing something to the python install by mistake)
I plan to convert my first system to use a jail as well when i get a chance.