While the DoD tends to be Microsoft centric (where departmental file, print, and email servers are concerned), the Naval command where I work currently does use quite a few Linux boxes. They are working on migrating off HP-UX to Linux. With the NMCI contract (EDS won a 5+ billion dollar contract to take over most IT functions from the desktop to the servers to helpdesk; however it only covers Microsoft technologies. Takeover is in progress) looming large, network admins are focusing more on their *nix boxes and hence linux (and even some freebsd).
As a software developer, it is nice to be able to have the choice of platforms. Don