The Beta Site is a back-up to the Alpha Site, a secret safe-haven and fallback position for Stargate Command (SCG) personnel and their allies.
When the Anubis' Kull warriors attack the Alpha Site, Colonel Riley orders the evacuation to the Beta Site. Not all of the occupants of the Alpha Site make it to the Beta Site. (7.16 "Death Knell") This is the only reference to a Beta Site in our universe.
Note: When Dr. Daniel Jackson goes through the quantum mirror to alternate universe, the Stargate Agency (counterpart to our Stargate Command) is evacuating their "Genesis list" to their Beta site. (1.20 "There But For The Grace of God" )
When Dr. Samantha Carter and Major Charles Kawalsky come through the Quantum Mirror to our reality, they report that before their command was destroyed, the personnel were evacuated and their Beta Site was told to bury their gate. (3.06 "Point of View")
--Torvac 14:40, 3 Mar 2005 (PST)