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I've heard that Seagate's Native Command Queueing (NCQ) technology makes 7200rpm drives more efficient than standard 7200 drives -- almost approaching that of 10k drives.
 
Read specs ...

See which one has the highest sustained transfer rate (mechanical limit) -- and which has the biggest cache.

Make a choice between the two.

Otherwise, the 3gb/s vs 1.5gb/s just means one depletes the CACHE twice as fast as the other.

Both drives SATA bus is much faster than the mechanical limit of the drive -- so all you are doing is making faster cache transfers.

Of course, seeing if you can match cache programming to your needs may also help ... since a cache miss will cost you dearly.
 
My question is that I have a Seagate SATA 250GB 7,200rpm with 16MB buffer, and my mac pro that should be here today only has an 8MB buffer. Is it worth my while to startup and run my main system on the 16MB drive or will I even notice a difference?
 
You should swap in your 16mb cache drive for your boot drive. The 16mb cache is beneficial because OS X will have more 'room' to store it's commonly used files. Thus, making your experience faster. Make sense?

By the way, the whole SATA 1.5 or SATA 3 is a marketing gimmick, currently, you can not even saturate or even come close to saturating a 1.5 drive.
 
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