I found a nice detailed post covering a NAS build using Windows and Flexraid. The author listed his reasons for building a custom NAS:
My main reasons for going towards a custom NAS were below
1. Ability to hook up USB drives to the NAS
2. Having a NAS where some storage places would be fixed like internal drives and some part would be mobile like in the USB drives which would be handy to carry everywhere (new arrivals)
3. Higher data throughput, helpful if you do a lot of copying in and out of NAS
4. Ability to run any UPNP Media Server of choice with media transcoding for supporting more variety of UPNP clients.
5. Better management options