I also recommend software RAID on Linux using mdadm over any fakeRAID. I have setup several NAS boxes with older motherboards (Pentium III and IV) where SATA was very limited and and used cheap SATA/RAID controller cards to use the latest SATA drives. I have always deactivated the fakeRAID settings in the controllers or on the motherboard on the newer boards. If the controller goes out, or you flash the BIOS of the motherboard you can hose your array in the blink of an eye.
I recently had an NAS Backup server with an old Pentium IV motherboard where I had 4 1TB SATA drives in a RAID 10 patched into a 32 bit PCI SATA/RAID controller. The BIOS went down and the system would no longer complete a post. The array was a software RAID running on Ubuntu 10.04 LTS Server. I was able to replace the motherboard with a much newer board with 6 on board SATA sockets. It took me 20 minutes to pull the old board and replace it, connect the drives directly to the mobo. Ubuntu spun up on the new board with out a problem and with the array completely intact. I think the only thing that got remapped was the NIC card which was now eth1. Linux software RAID (specifically mdadm) should work on any Linux distro with a Linux kernel 2.4 or higher (recommend 2.6 or higher).
I agree with Eric, image the Windows OS and restore/install it virtually onto the Linux box. This of course is based on the info provided.