This is a very nice discussion of these OS's and I just thought I'd post a couple of thoughts. I have run a series of custom built WHS 2003 systems in my house over the last few years. Plus, I've admin'ed a couple of Server 2003 and 2008 networks in addition to a couple of linux firewall \ file server systems. And most recently I've setup a Mini running Lion server at home. I currently have Freenas running on an older system to play around with from before I bought the Mini server.
WHS is a great product. Really, really great. I love it. I will say that the reliability isn't quite up to par since over the years I ran it I had to rebuild it a few times and more than once I had some data loss due to corruption. All this was on 2003, of course. Still, I loved it and still think its a great product. For a business with less than 10 pc's its pretty much an ideal backup system, imho.
Freenas is fine if you don't mind messing around on the command line. Personally, I don't use the CLI enough to be proficient on it so its always a little frustrating. But, it will certainly get the job done.
Right now I'm loving the Mini with Lion server on it. The power requirements are tremendous which is important on a system that runs 24\7\365. I got the base model and upgraded it to 8g ram and connected it via usb to an external drive for testing. So far its working fast and stable. I find the screen sharing to be much better than the RDP system from Microsoft with much better functionality when the machine is partially booted. Plus, the Lion gesture to just swipe to another full screen app is great and makes remote access to the Lion server fool proof.
I've installed uTorrent and iFlicks (my replacement for Handbrake) and found the combo to be just perfect. The system has easily handled transcoding for hours at a time with a minimum of noise and heat. Granted, it probably helps that I've got it in a closet just off my home office. Temps on the internal hard drive are reasonably low but still higher than my custom built setup at 33c. That's not high enough that I expect it to significantly shorten the lifespan of the drive but I'd still like to see it lower.
File sharing performance is reasonably good. I'm running a gigabit network which the Mini is directly connected to. The biggest use I have for the system is streaming multiple HD streams and it handles that easily. I haven't bothered benchmarking since I really don't care.
All in all, a Mini with Lion server fits Apple's motto of 'It Just Works!' and thats what I was looking for. Considering the price, power consumption (or, lack thereof), performance, size, noise and ease of use, I'm pleased to bits.
Anyone want to buy some hardware to build your own home server?