The EMP Control Center is one of the least captured buildings in the game. Why is this so? Well for starters its recharge time is 3:00. It's EMP lasts for 10 seconds, and it doesn't bring you any revenue. However, having this structure early game can easily change the tide in battle. Those few crucial seconds of your opponents units being under power can allow you to kill off some units, and improve your micro for when their units become un-EMP'ed. Here are a few guidelines when using the EMP.
Powering down an Armada
Timing is everything. Keep in mind that the charge itself only lasts for 10 seconds, and it takes around 2.5 seconds to fire. That said, if your opponents units are moving, you need to lead them with the EMP strike. Use the EMP when you begin to engage in battle. The blast radius is massive, so target as many crucial units as possible. Once the units are low powered, knock off the most threatening units first and work your way around killing the units that aren't powered down. That way you kill what is actually firing at you.
Powering down Air
The EMP itself takes roughly 2.5 seconds to actually charge up and fire. That said, you need to lead your opponents air units. The blast radius is very large, and one EMP could easily turn the tide in battle, as air units disabled with the EMP will crash and burn. Devastator Warships and Planetary Assault Carriers are invulnerable to this, when upgraded with their EMP-proof Forcefield Generators, but the EMP blast will disable the forcefields. On the other hand, the EMP structure is a great counter to a sneaky Mothership attack, as the slow and shieldless Mothership will be unable to escape from its blast.
Powering down Structures
In the likelihood that you are facing off against some massive Tier 3 Defense spam, an EMP to the frontlines may be just what the doctor ordered. With these fast few seconds, you can really improve your odds against a powerful lineup of defenses. Another option, would be to simply EMP your opponents power.
Combining With The E-Rush
When rolling forward with an Engineer Rush, knocking out your Opponents Construction Yard can prevent them from unpacking and therefore leave it open to be captured. Alternatively using it against the Construction Yard or Barracks can buy you the vital extra seconds needed to capture a key structure.