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Fundamentally it's the software (which can be added later), but you also get default hardware options more suited for server duty. It makes a bigger difference on the mini.
 
You pay $500 for an extra 2GB RAM ($30), an extra 1TB hard drive ($70) and OS X server ($20). Bargain eh?
 
Hello,
I want to know what's the difference between a mac pro and a mac pro server.

Pre-installed software and slightly different configuration. It also has in the past gotten you into a separate support queue. Aren't tracked into the "low common denominator" support queue if deal directly with Apple Support.
 
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