Hi Chris:
if you're interested in Department of Defense funding of academic research in the US, the quickest way to find this out is on the DOD website. It looks like there was a press release just last week regarding recipients of Multidisciplinary University Research Initiative funding:

http://www.defense.gov/releases/release.aspx?releaseid=14432

List of funded projects here:
http://www.defense.gov/news/d20110422MURI.pdf

I also see that the DoD has funded purchase of research equipment at academic institutions through a separate program (Defense University Research Instrumentation Program)
http://www.defense.gov/releases/release.aspx?releaseid=13410

These do not include scholarship awards to students, which may also be extended to support individuals (particularly grad students) doing specific kinds of research, and I suspect that that military funding may support academic research less directly in different kinds of grants.

Anyway, this may be a good place to start. Please feel free to give us more specifics about what you need if this doesn't answer your question.

Good luck with your research,

Bronwen