Mac OS X
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Mac OS X is the operating system on Gaius Baltar's computer at the Colonial Ministry of Defense (Battlestar Galactica: Origins 4).
Because of the "Macs don't get viruses, just install it" attitude as well as the latest version of Mac having the firewall off by default, this allowed a Cylon backdoor to be easily installed and executed on Command Navigation Program resulting in an easy defeat of the Colonial Fleet.
Pegasus was immune to the Trojan because the ship was still running on Mac OS X Tiger.
Galactica was immune to the Trojan because the ship was still running on vacuum tube computers and punch cards.