What can people do to defend against EMP? Does EMP affect all ships equally?

When you see an EMP about to detonate, you have three options - kill/disrupt the target (the EMP generator requires power to build up and maintain charge); get far enough away from the EMP blast to not be affected; turn off the components on your ship, so that when they get hit by the EMP blast, they will not be affected. That third option definitely favors multi-crew ships with engineers who are primed and ready to power cycle the ship at a moments notice.