Linux software raid
Becareful of WHS. There are reports of data corruption, but it is not intended for enterprise environments.
There is a much better solution called ZFS that runs on open solaris (and linux through fuse). It works on a JBOD level like a very sophisticated WHS with raid, backup, imaging, data integrity. This is the BEST solution for a NAS. Check wikipedia for some basic info and some links to the project site.
I'm building a linux based NAS/mediacenter and am very interested in software raid. It has better performance than hardware raid (raid controller) in the raid 10 implementation I'm going to use. You can still partition your drives any way you want. For example; on each 1tb drive you do 1x 10 gb, 1x 989 gb, and 1x 1gb partition. Then use software raid 5/6 on the big partition, raid 1(+0) on the 10 gb for OS, and raid 0 for swap in the 1gb partition. The os figures it all out with only a small penalty in cpu and memory i/o. You won't find any controller cards that can do that!