What I ended up doing was getting two 500 GB Maxtor Maxline Pros from OWC, one of their black dual eSATA enclosures, and the new Newer Technology SATA Cable Kit/PCI bracket that routes the two extra SATA ports from the Mac Pro's logic board to the back of the computer.

The drives were just $127.50 USD each, ($99 as of June 2007) the enclosure $67.95 and the bracket $24.95. I am in Canada. With the exchange rate, tax, customs, shipping and everything, the grand total when all was said and done was just under $500 CAD, a 50¢ per GB (in Canadian currency) cost for a fully bootable, dual-channel SATA RAIDable (software), 1TB of space in a slick black aluminum enclosure, shipped internationally. The shipping was literally <24 hours from ordering (i.e., I got my stuff in less than a day from ordering). Good on OWC and UPS. That's never happened to me before when ordering from US to Canada.

The build of the enclosure is beautiful, and echoes the design style of the Mac Pro. Installation of the drives is a breeze. Everything is machined with precision.

Where the process initially fell down, though, was when I went to install the PCI bracket/cables. I figured it would just be... plug in the leads to the logic board, screw in the bracket, good to go! But I opened the installation manual anyway. It said:
Remove the memory risers (whah??), remove four screws, remove your video card (huh??), slide the memory case to the right, unpop this plastic cover thing, then (get this) use a blank PCI slot cover (!!!) to shim and work off the fan casing! Remove the fan casing, unscrew the PCI slot support (towards the front of the case), remove all four internal drives, THEN (finally) plug in the leads, route the wires up around behind the hard drive bays, install the bracket, then put everything back.

Well, frankly, I was having none of that. I just reached carefully in behind the PCI slot support and fiddled until I got the leads plugged in blindly. (Also see later comments on this from another NT Cable Kit owner below. Hemostats are good to have around...) Screw routing the leads. They're stiff and just stay in the middle of the case nicely, not touching anything. Took probably 3-5 minutes of patient fiddling. I couldn't believe the major surgery they expect you to go through. Incredible. (I assume the instructions were for routing the cables completely out of the way? Or for better access to the motherboard ports?)

(He later sent some photos)

Here are some pics. Photographing where the leads plug into the logic board, however, is impossible. It is totally obscured by that pesky grey plastic (long card support/guide) thingy... :-)

Anyhow, I got everything hooked up and installed. Works great. Very, very fast, and I didn't even RAID0 them. XBench actually gave a single 500GB drive 98 MB/sec sequential read transfer rate, which is almost what my 2x250 GB RAID0 volume gets (old SATA1 drives, though). The enclosure fan is not too intrusive as long as you don't place the enclosure on any resonant object or space. On the floor, it is quite silent next to my Mac Pro which has 4 drives in it. Having them come up as two separate 500 GB drives works great, because I can back up my 500GB RAID0 media volume and my 500GB boot/download volumes simultaneously, all on separate SATA channels, so the process is very speedy.

The only "gotcha" I may have fallen prey to (gotta check this at home later this evening), is I think eSATA devices might not be hot swappable. That is, the manual says that eSATA devices are only detected at start up. I was hoping to be able to unmount the drives and power off the enclosure when not backing up, to save drive life and power (although, 5 year warranty and 1.5 million hours MTBF), and then just power up the enclosure whenever I wanted to backup. Maybe not able to? I'll have to check tonight. (BTW - there was post in the April 23rd news here with notes on Mac Pro onboard SATA chipset and drive swaps. I've mirrored it below to save a click. He later wrote.-Mike)
I tested it out, and I can unmount the drives just fine, by "ejecting" them in the finder, but when I power off the enclosure, a few seconds later I get a kernel panic (yes, my first one ever on my Mac Pro). This actually (ironically) worked out for the best. I ended up moving the enclosure to the laminate floor beside the Mac Pro, and now I can't hear the enclosure over the Mac Pro tower, so I just leave it on 24/7. Then I set up Retrospect to carry out a complete system backup every night at 2:00 AM. Worked like a charm last night, everything is cloned to the external drives. The drives still spin down, and for all intents and purposes, are seen as just two more internal drives to OS X.

Anyway, just thought maybe some other Mac Pro owners might be interested in a great cost-effective option ($400 USD... 40¢/GB including enclosure, interface and international shipping... less if you're in the States!).
-"Vader"

Reader Replies on SATA Cable Kit/Install: (most recent first)

(added 5/9/2007)
"I just finished doing this according to NewerTech's instructions - taking everything out, etc. as is described in your recent article. Let me tell you - they're not kidding when they say that Apple has fouled up in terms of making the memory bay mounting screws almost unremovable by using Loctite in the wrong place, effectively welding the screws to the standoffs they mate with.
(This was mentioned last fall on the early shipments, hopefully corrected on later builds. (It is per comments below from a more recent build Mac Pro.)
It's probably not practical for this area, but I've used heat to loosen loctite on some applications, but that was for screws on automobiles for instance where there was no chance of damaging adjacent parts - not in cramped quarters like this. It may not help, but if you have a (higher wattage) soldering iron tip you could try that to heat up the loctite. I don't own one of these to see if that's practical/would get the loctite hot enough to soften it. (The standoff may sink off heat depending on the base it's in and never get hot enough.) Not sure what grade (color) of Loctite they used either.-Mike)
It was simply not possible to remove one of the screws on my machine using a Phillips screwdriver even when stabilizing the standoff with a flat 7mm wrench slipped under the memory bay's bottom.
(I asked Seth when he bought his Mac Pro, to see if it was an early shipment)
Mine dates back to last fall - September, I think. That screw was no joke. Couldn't get it out any other way. No way to grab it with tiny Channel-Lock pliers or with a Vise-Grip, and I'm a handy type when it comes to such things.

I finally had to use a Dremel Moto-Tool with a carbide disc to slice a slot across the entire screw head so I could use a large straight-bladed screwdriver to get a grip on that screw and with tremendous effort finally withdraw it and get the memory bay housing out. I packed rags into the memory bay to keep grinding dust (there was very little) out of the logic board and CPUs. The rest of the install was straightforward. My suggestion: try installing the cables using a hemostat or needle-nose pliers with a little spaghetti tubing over the tips if you're nervous and bag the disassembly routine.
-Seth L."

(added 5/9/2007)
"Mike, I thought I would comment because I installed the kit the way they suggest by taking the Mac pro apart. It turned out to be not that big a deal, although i did hesitate at first and then took a deep breath and slowly followed the directions exactly, and it all worked fine. The good news is that the Mac Pro actually comes apart easily. (His Mac Pro is not an early build.-Mike) I didnt have to force anything.
The fan assembly is on a track and plugs directly into the board. The memory bay simply needs to be unscrewed and scooted over a tiny bit. All the parts inside fit into each other perfectly and come apart easily.

I would suggest plenty of light as there are a lot of very fine wires around the hard drive docks (Wireless/BT antenna wires) and you want to put the new sata wires safely behind them.

One issue noted in the manual is that on certain Mac Pros the bottom two screws in the memory bay had the locktite in the wrong spot and required holding the nut with a thin tool of some kind. I got mine a month ago and it did not have this problem.
I'm booting the mac from a Softraid mirror attached to the 2 new ports.
-Peter "

(added 5/7/2007)
"Mike, Thought I'd drop a line to echo Vader's comments regarding the Newer Tech SATA extender cable/bracket for the Mac Pro.

I installed mine much the same way Vader did - I didn't dismantle the Mac Pro's casing, but I will tell you I wasn't able to simply connect the cables to the motherboard posts blindly. I had to use a flashlight and a pair of needle nose pliers to seat the connectors. It was kind of a pain and took a good 10 minutes of trial and error, but it is doable. If you want to mount the cables more neatly or not risk scratching the motherboard with your needle nose grips, then following the (long) instructions is probably better.

I moved a (WD Raptor) 74GB 10,000 RPM drive out of the Mac Pro's case and into an external SATA case (OWC's single drive "quad" interface (SATA/FW800/FW400/USB 2.0) case). From both a performance and OS/Finder perspective, the drive may as well still be mounted internally. The BSD volume name is disk4s2 for those who are interested in such things.

Interestingly, while hard drives 1-4 are labeled as being in "Bay 1" and so forth by the Apple System Profiler and Disk Utility, these apps know enough not to label the two "external" ports as Bay 5 and Bay 6. The Finder icon is that of a standard internal hard drive, not that of an external, ejectable drive.

I haven't tried to dismount and power down the external case to replicate Vader's kernel panic. I think I'll take his word on this one.

I also have not yet tried to access a device on these ports in Windows via Boot Camp.

All in all, its a very slick way to add two more full-speed SATA II ports to your machine for nearly no cost.
-Cadaver"

A Copy of the April 23rd, 2007 news page post is below (in reply to eSATA Extender cables (w/PCI slot bracket) from Newer Tech for use with the 2 unused ports on the Mac Pro motherboard.)

" this may be of some interest for your readers.
From the Intel 631xESB/632xESB I/O Controller Hub data sheet:

"Hot-Plug Operation
Dynamic Hot-Plug (for example, surprise removal) is not supported by the SATA host controller. However, using the PCS register configuration bits and power management flows, a device can be powered down by software, and the port can then be powered off, allowing removal and insertion of a new device. "

(I asked if he knew of any way to do that in OS X.)
the SATA controller does support AHCI mode, which enables hot plugging (same as with the raid southbridges ICH6R - ICH8R which support hot plugging with raid drivers from Intel without Intel assuring this).

But it does not support AHCI if the PATA port is used as in the Mac Pro. And without AHCI there is no way to do hot plugging.

Using a SATA DVD drive may not mean AHCI is used automatically. The controller has to be switched from IDE to AHCI mode. Maybe the Mac Pro does it on startup or some EFI specialist can finds out how to do that.

BTW Tiger can handle an ICH8R in AHCI mode on all SATA ports without a problem.
Kind regards,
Martin S. "

Info/Tips on using Spare SATA Ports with Windows: (from Jan 15th, 2008 news page) This may have come up in the past and I'd forgotten it (don't own a Mac Pro yet) but in reply to a post yesterday (1/15/2008) on the Pioneer SATA Blu-Ray reader/Superdrive combo drive, a reader mentioned the spare SATA ports are not usable in Windows XP at least with the standard drivers with Bootcamp. (Most readers have used the ports in OS X although I've not searched drive db reports for anyone that mentioned using Bootcamp/Windows also. BTW - The spare ports are bootable for OS X use, as noted in this article - although drives are not shown/usable when booted from Windows with standard drivers.)
(Update) Here's a reader mail w/tips on using the spare ports with Windows via a replacement chipset driver install and grub bootloader edit:

" after finding this thread in the onmac forums I finally was able to get my pioneer sata drive to work under bootcamp. Basically you have to do the following:
- Install Win XP and ubuntu linux with a pata dvd drive in XP, change the ide 2680 driver to the intel ahci driver found here (downloadcenter.intel.com) S5000 Based Server AHCI SATA Storage Driver for Windows.
- Boot into ubuntu and change the stage1 file of the grub bootloader to this:
http://www.olofsson.info/grub/stage1
This keeps the mac pro in ahci mode when booting a foreign OS
Now you can boot windows using the linux partition, this will start grub and keep the mac pro in the correct mode

I also installed Refit to make things a little easier but as far as i know using Alt key when booting should work too.
if anyone tries this and has any questions feel free to ask
-Forrest"