http://www.dean.usma.edu/history/home.html
The mother of all map sites for Military History, this is the West Point Atlas at your fingertips. Great stuff

http://carlisle-www.army.mil/
The US Army War College at Carlisle Barracks site. Not so much history, but access to the latest publications and conference papers on things military.

http://www.fas.org/index.html
The Federation of American Scientists, again not too much history, but incredible for contemporary military policy, especially nuclear policy, etc. Used this site to show a visiting delegation of Chinese precisely where their ICBMs were. The party guy was not amused.

http://www.julen.net/ancient/History/Military_and_Warfare/
Part of the Ancient World Web site, it is really good

http://www.worldwar1.com/
A good source for World War I, but a commercial site so be advised

http://www.napoleonguide.com/
Likewise a commercial site on Napoleonic Studies

http://www.searchmil.com/
An interesting tool, but again ultimately commercial, so be advised