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Most Stack Exchange sites started off as Area 51 proposals, passing through the definition and commitment stages there before moving on to become beta sites and perhaps graduated ones.
Presumably the flagship site SO, and perhaps some of the other oldest sites like Server Fault and Super User, didn't pass through this process. I believe some of the unusual outlier sites, like Stack Apps and CS50, also didn't pass through Area 51.
What is the complete list of Stack Exchange sites which didn't start in Area 51?