1.JLA Satillite: The best HQ in all of comics.
2.Fortress of Solitude: The most famous headquarter with the acception of the Batcave.
3.Baxter Building:Reed has more high tech toys than anyone.
4.Batcave:Not as flashy as Supes hangout,but it's state of the art.
5.Stark Tower: Tony spared no expence.More high tech than the batcave,but not as popular.
6.Dr. Stranges Sanctum Sanctorium:It on weird place,with door to other dimension and such.
7.Fate Tower:Same applies her with Fates hang out.Wonder were its located.
8.JSA HQ: I pick up my first JSA book not too long ago,they have a pretty nice hang out with everything the Satillite has.
9.Nick Furys' Safe Houses:Fury is one of the best planners in comics along with Cap and Batman,he has state of the art safe houses all over the world that not even Shield knows about.
10.X mansion: As a HQ it serve them well,but it leaves the Xmen too vulernable,too out in the open.