Presuming it has a remote trigger, what methods are available to insure a cortex bomb doesn't go off?
Haven't read all the other responses. Here's my list.
Faraday Cage - Unless the trigger is a dead man's switch setup where lack of signal for a certain length of time sets it off, someone in a faraday cage can't get the trigger signal from outside it, period.
Brick it - Matrix 101: A device that does not work, can't be told to explode.
Hack it - Matrix 202: A device that has its access codes changed can't be set off with the old codes.
Surgery - Unless it has anti-tampering software, cutting the thing out works. Of course, you need the skills and setup for that.
Turn to Goo - An old favorite. I remember it being talked about for stealing a Street Sammy's wired reflexes and other expensive ware back in 4e (the actual question was based on 'oh god, what happens to this person after that', but still), but it also works for getting a cortex bomb out of the guy's head. Remember, though, that the guy who used to have a cortex bomb is now going to have a hole in his head where that mass used to be.