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.