The Collaborative International Dictionary of English v.0.48:

Headquarters \Head"quar`ters\ (-kw[add]r`t[~e]rz), n. pl. [but
   sometimes used as a n. sing.]
   1. The quarters or place of residence of any chief officer,
      as the general in command of an army, or the head of a
      police force; the place from which orders or instructions
      are issued; hence, the center of authority or order.
      [1913 Webster]

            The brain, which is the headquarters, or office, of
            intelligence.                         --Collier.
      [1913 Webster]

   2. The main office from which an organization such as a
      commercial enterprise is managed; -- usually where the
      chief executive officer works.
      [PJC]

WordNet (r) 3.0 (2006):

headquarters
    n 1: (usually plural) the office that serves as the
         administrative center of an enterprise; "many companies
         have their headquarters in New York" [syn: headquarters,
         central office, main office, home office, home
         base]
    2: the military installation from which a commander performs the
       functions of command; "the general's headquarters were a
       couple of large tents" [syn: headquarters, HQ, military
       headquarters]
    3: (plural) a military unit consisting of a commander and the
       headquarters staff

Moby Thesaurus II by Grady Ward, 1.0:

34 Moby Thesaurus words for "headquarters":
   CP, GHQ, HQ, base, base of operations, booking office, box office,
   branch, branch office, cabinet, center of authority,
   central administration, central office, central station, chambers,
   chancellery, chancery, closet, command post, company headquarters,
   consulate, corporate headquarters, den, embassy, executive office,
   general headquarters, home office, legation, main office, office,
   seat, shop, study, ticket office