TrueNAS has support for HA (high availability). That is nothing more than 2 systems that share a common pool. One system is active and the other is passive. If the active system goes down the passive system picks up the load immediately. Downtime during failover is less than 5 seconds. This feature isn't available on FreeNAS at all.
TrueNAS is an appliance, so it comes loaded on custom hardware built/designed by iXsystems. There is no option to run TrueNAS on your own hardware.
TrueNAS also has no jails as TrueNAS is sold as a file-server exclusive appliance.
TrueNAS also has optimizations and features such as jbod chassis management and such that are only offered on TrueNAS because they are custom code specific to the exact hardware iXsystems uses.
Buying TrueNAS basically gives you white-glove support for your file server. You have a problem you call the support number and iX makes the problem go away (sometimes I picture in my head a video clip of the head of the mafia pointing at someone and saying "make this guy disappear" and the guy disappears). That's how TrueNAS problems are resolved. Some people ask us to create datasets for them because they'd rather we do it. Others are comfortable creating their own zpool with the volume manager and doing all of the setup themselves. The iXsystems support team will provide as much or as little support as you need for your TrueNAS server.
If you want to just buy a file server appliance that uses ZFS and informs you when something is wrong, and you call a number and say "make this problem go away", then TrueNAS is hands down the way to go. TrueNAS users aren't expected to be masters of using TrueNAS (and technically FreeNAS since they are mostly identical), but some choose to be.
Buying TrueNAS makes any problem you have with your server iXsystems' problem, whereas going with FreeNAS makes any problem you have with your server your own problem to solve on your own. By far and away when I've talked to people that have just started using TrueNAS they were absolutely shocked at how fast our support turnaround time is, how much support we are willing to provide, and how much effort we put into making sure that the owner of the server is 100% satisfied with their purchase.
I talked to one person today that bought a TrueNAS box and he had some networking problems right away (they weren't our fault, but we provided support to help him troubleshooting the problem). He couldn't believe how much support we were offering and he said he's got about a dozen other file servers he will definitely be looking to move to TrueNAS in the future. He was using Netapp and said that he's done using Netapp after the support we've provided with the first TrueNAS server he bought. ;)
I had serious reservations about providing support for iXsystems' customers because too many companies are ready to throw their customers to the wolves and be all "it's your problem, deal with it yourself" but I've been shocked by the quality of support that we are expected to provide and it is very satisfying to know that the support team at iXsystems are expected to provide a level of support that is far and above what other companies are willing to do. I've done support before when I was in the Navy and they were so quick to throw the customer to the wolves I never wanted to do support again. That's just not a way to treat someone, customer or not. But iXsystems has a vested interest in making you happy on day one and keeping you happy for as long as possible.
Edit: If you want to talk to someone about TrueNAS you can call and ask for me by name or talk to the sales team. The sales guys know a lot more about selling file servers than you'd expect. They know when an slog is useful, when an l2arc is useful, whether you want mirrors or a RAIDZ2, etc. I really expected that the sales department would be a bunch of drones bent on selling hardware that wouldn't be adequate for most people's needs because of the complexities of ZFS (let's face it.. ZFS isn't easy to master). But I'll be damned if they don't have their act together and do expert hardware selection!
Another edit: People seem to find this post from time to time. Please note this post is from January 2015. Features are added to TrueNAS with each build, so please do not assume that this information is 100% accurate. If you want to know what the current state of TrueNAS is, visit the website
www.ixsystems.com/TrueNAS or contact one of our sales people. They can answer any questions you may have on currently supported features, etc.