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It comes with a vastly superior OS. It will be interesting to see what those resale values do when people realize that you should be able to take an old windoze box, format the hard drive to get rid of the windoze crap, and mount OS X written for a CISC processor on it. You could, of course, skip Apple's implementation of the BSD version of Unix and go straight to Linux (which I've done) but Linux doesn't have brand recognition that Apple does.
(this was processed by an Apple G5)