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What operating system do the Apple TV models use? Do they run Mac OS X? Do they run iOS?
When the original Apple TV was first announced as "iTV" on September 12, 2006, it appeared that the device was running a "stripped down" version of OS X. Upon its release, Walter Mossberg in the WSJ confirmed that the Apple TV uses a "modified version of the Mac operating system".
The operating system on the disk is a stripped down version of OS 10.4.7. . . There is at least one partition for the operating system which is mounted as read-only (the second is where all of the media files are stored, [and] a third contains a fresh copy of the OS for factory restores).
The original Apple TV was not intended to run a "full" version of Mac OS X, but mere days after it shipped, creative hackers developed a way to run a full version of Mac OS X on the original Apple TV, as well as run the "Apple TV OS" on a MacBook and a PC.
The black Apple TV 2nd Gen and Apple TV 3rd Gen models have a completely different architecture -- each is similar to an iPod touch without the display rather than an Intel PC -- and although neither formally runs iOS, both run a variant of the same iOS operating system that powers the iPod touch, iPhone and iPad models.
The Apple TV 4th Gen (Siri) runs yet another operating system, which Apple refers to as a new "tvOS." When it first shipped, Everyi.com hand documented that the device self-reports tvOS 9.0, build number 13T396a.
Officially, the original Apple TV is not designed to run any Mac OS X "applications" other than the software pre-installed and fine print on the Apple website at the time of the Apple TV's release noted that "iPod games will not play on Apple TV." However, hardworking hackers reported that they were to get some Mac OS X applications running to varying degrees of success on the original Apple TV including iTunes, VLC, Joost, Firefox, and even World of Warcraft using the default operating system as well as a "full" version of Mac OS X.
Neither are for beginners, but Tutorial Ninjas has more information for adventurous users who are willing to void their now long expired Apple TV warranty and attempt to run Mac OS X software on the original Apple TV using the original operating system and AppleTVHacks.net has a tutorial with details on how to run the full version of Mac OS X.
The black Apple TV 2nd Gen and Apple TV 3rd Gen have a completely different architecture than the original model and cannot run Mac OS X or Mac OS X applications. These cannot run iPod games written for the pre-iOS powered iPod models and are not intended to run iOS applications written for the iPod touch, iPhone or iPad models either. They do have a variety of pre-installed "channels" that function somewhat like apps, though.
Finally, the Apple TV 4th Gen (Siri) offers a full third-party app library for the potential of a wide variety of native apps and games.
The original Apple TV was not intended to run operating systems other than the one pre-installed on the system. However, as it uses a standard Intel architecture, the underlying hardware is capable of running Windows and Linux and creative hackers have been able to do so.
Subsequent Apple TV models are much more "closed" and there have been no known efforts to run Linux or other alternate operating systems on these systems.