I experiment with FreeNAS recently, and it is quite simple to start and shut-down it automatically: whenever a client on the home network logs into Windows, it sends WOL signal to the FreeNAS PC, therefore, data are available in about a minute (unless I can figure it out how to place all user profiles on FreeNAS, it is not a big delay, Windows isn't too fast either). On the other hand, a simple FreeNAS script pings all PCs on the network every 10 minutes, and if no PC answers, FreeNAS shuts itself down. In this way there is no need for pre-scheduled start and shutdown, and the whole process is completely transparent to the users.
As I'm getting more familiar with FreeNAS (I just finished adding virus scanner and plan to add the torrent client, checking out wake-on-WAN, remote backup, etc.), this ping approach will not be enough to decide on shutdown, but for a Windows guy like me it will take a while to figure these things out, and hopefully then I will be able to modify the shutdown script to check the running processes before shutting FreeNAS down.
Anyway, why run the file server if there is noone around to serve to?