I just finished a similar upgrade and here is what I did.
From Other World Computing I purchased a NewerTech MaxPower eSATA 6G PCIe 2.0 Controller with 2 eSATA ports. This is a plug and play controller that works with the AHCI standard interface. No additional driver needed. This card does not support port multiplexing so I can only have 2 drives online at a time which is all I required. This was about $50. If you need more drives online than they also sell a Sonnent 2 port card for about the same price that will do port multiplexing so up to 5 per conection.
Also from OWC I have been buying Hitachi DeskstarTM 7K1000.C drives. The 7K100 drives are very quiet and fast. The "B" version had 3 platters and the new "C" version has only 2 platters and run fast and quiet.
OWC is a great company to work with. A year ago I purchased a pair Seagate drives and both of them had enough vibration to make my Mac Pro hum when it was running. They first dropped shipped my a replacement and then when that one also had the same problem the exchanged the Seagates for Hitachis with out any hesitation.
For an external case I purchased a 2 drive case with trayless slots from Mac Gurus. This one does not have a port multiplexor but they also have cases with 4 to 8 slots if you need them. I love the trayless design as you can just slip in a bare sata drive in and out of slot. No extra "proprietary" trays to purchase for each new drive. The only down side is this case has 3 fans and it is at least to my sensibilities quite noisy. But since I run it only for back up operations it is not a big problem. I searched all over and these are the best price cases I could find.
To store my bare drives I purchased some of the Wiebetech static boxes that Peter shows in his book.
Finally I also purchased a WD VelociRaptor 600GB drive as my new system disk. This is the fasted HD you can buy today and it has made a huge improvement with my system responsiveness. It just takes a fraction of the time to boot and load applications than it use to. Lightroom used to take 20 seconds to load not it is less than 5 seconds. This is a new drive and I finally found one at newegg. They were limited to 1 per customer last week.
Here are sources:OWC Hitachi 1TB driveNewerTech ControllerMacGurusWeibtech CaseNewEgg