I second the Spy Museum. rhysara and I hit it, it was great. The hours are a bit funky though, and you have to get a ticket (they let people in hourly, I think.. its quite popular and they have to limit the inlet rate to keep the place from getting too crowded).

And as rhys pointed out, the National Postan Museum (across the street from Union Station) is actually pretty cool.

If you've got a car, I hear the NSA even has a museum these days.