There’s some good plugin documentation available on the FreeNAS website explaining how to use the plugins, how to install the plugins jail, how to create, find, install, and configure PBIs, such as Firefly, miniDLNA and Transmission. If there’s no PBI available (yet), the page shows how you can create your own PBIs, and how to install non-PBI software using the FreeBSD ports and packages collections.
Plugin support is still a bit crude in FreeNAS 8.2, but it is looking a lot more polished in the upcoming FreeNAS 8.3.
FreeNAS 8.2.0 Plugins Part 1: Installing
FreeNAS 8.3.0 Plugins Part 2: Plugins Configuration