The Pegasus Alpha Site is an outpost set up by the Atlantis expedition as early as their first year in the Pegasus Galaxy. The original Alpha Site was abandoned after being discovered, and tagged, by the Wraith and the expedition had to search for a replacement.
A new Alpha Site was set up in the second year and was used as a temporary prison (and research) facility for the Wraith known as Michael Kenmore. This base was likely abandoned after Michael escaped and returned to the Wraith. (SGA: "Michael")
In 2008, the Atlantis expedition was considering the Flying monkeys' planet as a possible Alpha site. (SGA: "Ghost in the Machine") It is likely the Alpha site is used and built in the same way as the one in the Milky Way Galaxy.
Known planets for the Alpha Site: