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Yes. The license covers all of your Macs.

App Store purchases for private use do. A "free Mountain Lion upgrade", for example if you purchased one Mac just before Mountain Lion was released, probably doesn't.

On the other hand, I doubt that Apple cares much about that as long as you pay good money for their hardware.
 
I purchased a Mac before the release of ML and have gotten a free license (it's actually a redeem code for ML in the MAS). That license is the normal MAS one so I'm entitled to run it on each Mac I control or own. The Macs that come with ML are not the MAS version and are bound to that machine only (it's the preinstalled copy). You are not allowed to use it for virtualisation or to run it on other Macs. If I recall correctly it also won't show up on the purchases tab in the Mac App Store (the people who've gotten a free license will see it there). This is also clearly stated in the OS X license agreement (sections 2A, 2B and 2C).
 
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