Most military weapons systems rely on sophisticated electronics for control, so if you can somehow knock out the circuits, the weapons will become useless. A new type of missile tested last week by Boeing and the USAF exploits this vulnerability, by zapping selected buildings with microwave energy so powerful that all electronics inside will stop working.
Boeing's CHAMP (Counter-electronics High-powered Advanced Missile Project) missile was flown over a test range in Utah, where a two-story building was set up with a room full of operating computers. The team directed CHAMP's microwave beam towards the building as it passed, and all of the computers quickly went blank. In fact, every electronic device in the building was disabled, including the cameras set up to monitor the results.
The idea is that you can disable your enemy's response capability, without causing a massive loss of life or damage to buildings and infrastructure. Still, I suppose they could always wrap their command center in a Faraday cage, and what would happen if the enemy uses the same methods to knock out your CHAMP missiles?
Check out the video to see the results of the test. Note that one computer in the back of the room even spits out its CD-ROM in surrender when it gets hit by the pulse.