After reading your post I have a couple ideas...
Data drive:
2x 1TB in RAID1 is a good start, and since Linux is more flexible than Windows, you could set up the RAID 1 on the on-board fakeraid controller. Format it for NTFS like you mused, and use the dm-RAID facility on Linux, combined with ntfs-3G to be able to mount and read the partitions from there.
OS drive:
Once you migrate your data from the 320GB RAID 1 to the 1TB RAID 1, why not split the 320s, and use one for Linux and one for Windows? After that, you could weave the 2 80GB drives into a RAID0 scratch drive, or as a swap space for Linux...
In fact, you could put the two 80GB drives into an external 2-bay enclosure and use them as a (smallish) data safe.
Data drive:
2x 1TB in RAID1 is a good start, and since Linux is more flexible than Windows, you could set up the RAID 1 on the on-board fakeraid controller. Format it for NTFS like you mused, and use the dm-RAID facility on Linux, combined with ntfs-3G to be able to mount and read the partitions from there.
OS drive:
Once you migrate your data from the 320GB RAID 1 to the 1TB RAID 1, why not split the 320s, and use one for Linux and one for Windows? After that, you could weave the 2 80GB drives into a RAID0 scratch drive, or as a swap space for Linux...

In fact, you could put the two 80GB drives into an external 2-bay enclosure and use them as a (smallish) data safe.