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Component vs. System Performance
As with every component of the PC, the hard disk is but one part of an integrated whole. It is not possible to measure the performance of the hard disk in isolation, since running any benchmark program involves using the processor, memory and other parts of the PC. The only way to isolate the hard disk would be if you were to use specialized test hardware, connected directly to the hard disk itself, and then you'd have a hard time being sure that the results really related to "real world" PC performance at all.
Many benchmarks are designed to try to isolate the hard disk from the rest of the system to test "only" the hard disk. Some are more successful than others in doing this. Unfortunately, many of them don't take all the factors into account and end up (for example) testing the system's hard disk cache instead of the hard disk itself. They are getting smarter over time, however, but still, virtually every hard disk benchmark I have ever seen has allowed the rest of the system to impact the number. You take the hard disk out of a Pentium II 300 PC and put it into a Pentium III 600 system, run the benchmark again, and the score goes up.
As with other components, the best way to compare two hard disks is still a comparative benchmark. Set up the system they are intended to be used in, test one with a benchmark that represents the intended use, and then replace it with the second drive, retest and compare. This eliminates much of the "background noise" that is associated with absolute benchmark numbers. Most better review sites do exactly this, maintaining constant "test benches" with hardware that does not change between tests of various drives.
Another thing that the matter of "component vs. system" means is that there is no way to (legitimately) compare directly two drives that run under different interfaces or in different systems entirely. In particular, you can't directly compare the speed of an IDE/ATA drive to that of a SCSI drive and be sure that you are measuring only the drive. Some would rightly point out that the distinction isn't really that important however, since the "end result" of system performance is really most important.
As discussed here, hard disks have a very substantial impact on the performance of the system as a whole.