Your Alpha Complex: A blog post written by Costin-U-MOR; provides useful "hooks" for creating your own alternate Alpha Complex.
In Nomine is an RPG where players are either Angels or Demons fighting a cold war over the fate of the Human race. Surprisingly, there has been many attempts to adopt Alpha Complex into this setting, usually treating The Computer as "God" itself. Even if you are not interested in "In Nomine", these three links should at least give you some useful ideas for creating a hyper-religious Complex.
Alphaville is a proposed alternate Alpha Complex setting that takes place in the 1950's. A potential hook for a campaign, inspired by Phillip K. Dick.
Bubblegum Complex is an alternate Alpha Complex that shares superficial differences with that of Alpha Complex (different secret society names, schooling system changes, salary and living expenses, etc.). Still very useful if you want a rival Alpha Complex that looks the same, but is slightly different.