Beginning with 8.1, FreeNAS will support the installation of software packages through the use of a plugin system. These packages will be in the form of PBIs (Push Button Installers) which is the packaging system used by PC-BSD.
There is a PBI forum where you can request the creation of PBIs. If there is an application that you’d like to see available for FreeNAS 8.1, read the README on the PBI Request Forum first as it contains instructions for determining if a PBI already exists and, if it does not, how to request that a PBI be created. More information about how the PBI request process works can be found in the PC-BSD Handbook.
If you’re interested in trying to create your own PBI, use the instructions in this page of the PC-BSD Handbook. It is important to note that the PBI format will be changing between versions 8.x and 9.x. If you are interested in creating a PBI for FreeNAS 8.1, follow the 8.x instructions.