I have two WD400JB's ordered with Newegg right now. I wanted to go with some of the deals available now for like the 200GB Maxtor at Dell, but the rebate is limited to one, or the Staples 160GB drives but they're out of stock (and probably limited to one on the rebate too anyway). 400GB storage space would have been complete overkill, the drives would fail before I could use that, but the price couldn't be beat, and if I used only my usual 20GB or so, it'd be the fastest partition ever since the entirety of it would use like 2% of the tracks.
But since I couldn't get those, and I'd made up my mind to get started with RAID again, the WD400JB was the best deal for my needs. I'd have even gone with two 20GB drives if they'd had 8MB cache versions. I've only got two 20GB partitions right now, and they're only half full. Two 80GB or 60GB drives would be a better value, but since I would never use the space, the lower overall cost of the 40GB works better for me.
I'm also going to use a Promise Fastrack TX2000. Most ATA RAID controllers are not full hardware processing devices, they're "software controllers". The TX2000 does almost everything onboard rather than through the CPU, so the hit on CPU time shouldn't be as great. Even if it is, my board doesn't have a PATA RAID controller, and I didn't feel like moving to SATA which I do have, because the performance won't be much different but it'd cost more.
HyperThreading won't be affected by using RAID. As far as the OS is concerned, there are two CPUs in use, and one single drive connected to the controller. Neither the logical CPUs nor the OS care about the physical drives.