Okay, lots of stuff to respond to.
The driver only "comes with" the SATA adapter if you are trapped in the Windows prison. On Linux, FreeBSD, et al the driver authors and the hardware vendors are orthogonal. So it's possible to have command queueing even if the Windows driver does not support same.
Secondly, I think it is too bad that software RAID wasn't tested. Quiz: what makes a better RAID processor, 1) an Opteron 244, or 2) an Intel i960? If you picked 1, you picked correctly. And the Mylex 170, what a dog. It does not exactly have a reputation for speed. Software RAIDs will blow its proverbial doors off.
Also it is easy to disable or limit command queueing on some SCSI HBAs. On Adaptec HBAs the depth can be clamped anywhere between 0 and 255, on a per-target basis.
I do take some minor issue with how the article is presented, especially its conclusions. I think the definition of single-user or desktop user is vague. Many people do absurd operations on their personal computers that would make some servers blush. I personally have a PostgreSQL database that exceeds a terabyte, and I like to compile very large trees of software. I use a RAID5, because I dislike losing my data, and there is a significant benefit to compile time from the RAID setup. The RAID5 setup also improves performance on metadata-intensive workloads, like tar/untar or cvs update.
Finally, thanks for a nice article with some good hard data.