I think that we're going to learn a lot from the kind of work discussed in THIS ARTICLE.
I'm frankly amazed that the only military applications thus far are for possible non-verbal communication between soldiers. Maybe that's because the technology is pretty crappy (much of it does not work well with about 30% of people; and for those who can use it, the error rate is still very high). The trick I think is going to be to use these technologies to assist rather than all by themselves. I think something similar happened with the artificial heart. When put in as a heart replacement the recipient never lived very long, but when scaled back to just assist the original heart the technology did a lot better. So the trick will be to see how the various measurements of brain activity can be incorporated into existing human computer interfaces rather than attempting to replace them.
Here's three crude examples. (1) Assume that heightened alpha waves correlate with better ability to operate remote operated weapons. If you could put into the regular interface for the training machines of these weapons the kind of feedback mechanisms to heighten alpha waves, and incorporate that into the weapons themselves, then you'd get a better weapon system. (2) Perhaps some kinds of brain states correlate with dangerous inattention. A pilot's helmet could measure for this and ring an alarm. (3) I hate to mention interrogations, given the horrific news that has been coming out about American violations of the Geneva Conventions, but here goes. It will probably never be the case that a machine can automatically tell if someone is lying. But it seems plausible that this brain-computer interface work at least has the potential to produce pretty good tools to assist in interrogation of suspected criminals.