I had been researching my Mac Pro for many months while I saved my pennies. At the time my setup was a macbook with 4 external hard drives, One x Lacie Firewire, 2 x cheap DIY USB 2 drive cases, and one a Western Digital Mybook with Usb 2 & eSata. I figured once my new Mac pro arrived I would throw away the cheap usb cases and place the drives internal, and the Lacie & Western Digital external for backup reasons.
Never being overly happy with USB 2, I really wanted to be able to use the eSata connector on the drive. During one of my googling sessions I came across a page over at Macenstein (yes a page other then "Mac Chick of the Month"), praising Newer Technologies Mac Pro eSata Extender. Now you can get numerous PCI-X cards with eSata connectors on them that will work in the Mac pros but what's different about this one, is it uses 2 "hidden" sata connectors on the mother board.
I say hidden because these sata connectors are behind the fan assembly. Newer Tech supplies step by step instructions for both first gen Mac Pro's and the 2008 Mac Pro. The instructions from Newer Tech where easy to follow and in the case of the 2008 Mac pro there are just 2 screws that need to be removed. The other pieces of the puzzle are all screwless, hard drives, fan assembly and processor cover. Please note this may differ in the first gen Mac Pro. The instructions also tell you to remove the GPU but I can not see any reason why this is required. Once installed tuck the sata cables behind your hard drive mounts and reassemble.
The Newer Technology eStat Extender, was simple to install. Start to finish maybe 10 minutes. As the eSata extender is made for the Mac Pro the cables are the exact length needed. here is a hint for anyone thinking of doing this, run you machine for 10 or 15 minutes first, this in insure the mac is warm but not hot and the fan assembly will slide out much easier (thanks to dotnet for the tip it worked a treat).
The only downside to be aware of kiddies is that eSata is not hot swappable like firewire or usb. If you unmount the drive and disconnect you will need to restart the machine to get it recognised again. Also make sure your power lead to your drive is safely out of the way of the wife's hoovering, A bumped power lead while doing a superduper clone to the machine can cause a kernal panic, so I found out.
But with that one downside having the speed of eSata sure does improve the performance of the drive.
Firewire 800 eat my eSata dust

(Please note: picture credits go to macenstien, I didnt take pictures while installing mine sorry)