Blackhawk Island, base of Blackhawk’s team:
There have been several different Blackhawk Islands over the years. Blackhawk Island is the home base for the Blackhawks, a paramilitary group founded during World War II. Blackhawk Island houses the members of the Blackhawk Squadron, their planes,...
Challengers Mountain, HQ of the Challengers of the Unknown:
And the Green Lantern Corps gets the entire planet of Oa as HQ:
Oa is a fictional planet that lies at the center of the DC Comics universe. Since its inception, Oa has been the planetary citadel of the Guardians of the Universe and headquarters of the Green Lantern Corps. It first appeared in Green Lantern (vol. 2) #1, when the Guardians summoned Hal Jordan's "energy duplicate" so they could hear of his origin.
One of the oldest planets in the universe, Oa serves as the home and headquarters for a race of blue-skinned powerful humanoids called the Guardians ...
The New Champions in Austin Grossman’s tragicomic superhero novel Soon I Will Be Invincible have a high-tech HQ in midtown Manhattan.
Yup:
The Transcontinental Airway System was a navigational aid deployed in the United States during the 1920s.
In 1923, the United States Congress funded a sequential lighted airway along the transcontinental airmail route. The lighted airway was proposed by National Advisory Committee for Aeronautics (NACA), and deployed by the Department of Commerce. It was managed by the Bureau of Standards Aeronautical Branch. The first segment built was between Chicago and Cheyenne, Wyoming. It was situated in t...
http://www.stgeorgeutah.com/news/archive/2013/09/07/jt-washington-county-points-the-way-from-salt-lake-to-l-a-1920s-navigational-cement-arrows/#.WaQlpz6GOUk
The Champions of Los Angeles (Marvel) had a headquarters building that, in a running gag, nothing worked right. Turns out the contractor low-balled all the bids and made the headquarters with cheap materials.
Not quite a building, though.
Didn’t though the Green Lanterns have some sort of great hall on Oa? Marv Wolfman era? The giant sized special issue with Nekron and the red robed GLs?