The various government agencies each have their own official travel agent.

GSA city pair carriers and contract fares:
http://apps.fss.gsa.gov/citypairs/search/

These are only for official travel.
Joint Travel Regulations:
http://www.access.gpo.gov/nara/cfr/w..._03.html#301-1

When combining official and personal travel, the latter segments must not be at contract rates. Misuse of government contract fares is grounds for discipline, and the abuser will be held liable to pay the difference.

As stated in other posts above, hotel rates are mostly done on a courtesy or marketing basis, not negotiated by the General Services Administration.

Anyone aware of misuse of government contract rates or other travel malfeasance by either employee or contractor can report it to the office of the Inspector General for the affected department:

http://www.ignet.gov