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Hard drive speed, hard drive speed, hard drive speed. The fastest laptop hard drive is still painfully slow compared to any decent desktop hard drive. This is really apparent on things like compiles where you are accessing thousands of small files scattered all over the drive.

The newer 7200rpm laptop drives aren't too bad for speed now. They're still not as good as a desktop but it's a major improvement over old 5400rpm and 4200rpm laptop drives which just crawled along.

You can always tote an external USB2/IEEE1394 HD around if you want fast access. Some Mac mini users use an external IEEE1394 desktop drive as their boot drive and they apparently get huge speed increases because of that.