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AFAIK Apple uses a variety of different brands for their HDDs so unless this is specifically different cause it's the MP, I think it varies.
 
It's gotta be the WD6400AAKS since no one else makes a 640GB drive as far as I know.
edit: i stand corrected
 
Why would you be disappointed in the WD1001fals? Isn't that the better Caviar Black lineup, with 32MB cache etc:

http://www.wdc.com/en/products/products.asp?driveid=488

As opposed to the mid range Blues like the WD6400AAKS with 16MB cache:

http://www.westerndigital.com/en/products/products.asp?driveid=394

By the way, Mike at xlr8yourmac received the WD6400AAKS you were hoping for:

http://www.xlr8yourmac.com/systems/2009_MacPro/2009_MacPro.html

Wait I'm asking about the 640gb hdd models not the 1TB ones from Apple as a BTO.
 
Right, what I'm saying is that personally, I would have hoped it was a Caviar Black series (ending in ALS like the 1 TB model mentioned), not the Blue series (AAKS models). In other words, this would have been my stock 640 of choice:

http://www.wdc.com/en/products/products.asp?driveid=551

Here's a good comparison of 640 GB HDs at X-bit (17 pages!):

http://www.xbitlabs.com/articles/storage/display/640gb-hdd-roundup.html

To quote them: "Do you want the fastest drive for a home computer? Take a Western Digital Caviar Black." But they liked the Blue for a server, so depends on your use.
 
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