Hi ant900,
The short answer is that since FreeBSD doesn't actually support the RAID functions of the Intel ICH chips your only choice would be to use one of the RAID options in FreeNAS. Depending on which version of FreeNAS you run there are a number of choices you can use, assuming you have (or can put together) a fairly modern system that supports 64bit and can get more than 4GB of memory together, ZFS is the way to go.
Pretty much any RAID worth using is going to "tag" each drive with something like "Drive X of Array ZZZZ" so moving from some hardware to another shouldn't be to troublesome. With ICH RAID you would of course have to move to another Intel ICHR board, but it should see the RAID. Same thing with ZFS, only you don't need to worry about matching hardware, as long as you can hook up all the drive it ought to be able to import the array information.
-Will