What you should always do is test something which is as similar as possible to what you care about.

That's all it comes down to really.

In this particular case, the big-iron machine *is* slower than your desktop for a single-threaded load (as others have pointed out).

If what you care about is a non-parellisable problem, your home machine *will* run it faster than the big box.

If what you care about is producing numbers which show your big box is fast (which is fair enough, it's fun to play with these things), then do what the others mentioned and run multiple cpu crunchers and aggregate the results.

But this is only CPU, of course. If your problem has a 2Gbyte dataset, the desktop has 1Gb RAM and the big box has plenty, then you'll see a big difference depending on how much RAM you use in your performance test.

So...perf comparisons between hardware come down to how accurately you can model the load you care about. Which is generally limited to how well you understand it and how well you can reproduce 'real world' conditions. (A thousand users on slow modems nibbling away at your app, plus 10% on screaming broadband can produce a very different load to 100 looping procs on another box on your LAN).