Final Flight of the Osiris Explosion....

I love the scene part Don Cheatle holds his skivvies

I'm not really just narrowing my suggestion to EMPs though, I'm also thinking of the guns, such as the one used by Cypher and Agent Smith.... that shoot an electric blast out. Would be good for mounting outside the ship... and I'm guessing it would lead to a chain attack effect on multiple machines in close proximity?

Not to mention damaging/diabling the ship the guns are mounted on.

That and something gives me the idea that they're only effective at short range.

Let's also not forget that these guns will be a considerable power drain. The ship may end up just losing the ability to defend itself due to the lack of power needed to fly and defend the ship.

Well the guns are easy to make, the electric guns aren't, I assume or everyone would have one. Secondly there is no place for the guns in human hands because the caliber is too big. Thirdly, guns pump out enough hot leaden destruction to slow hordes of sentinels down.

Oh yeah and I don't think the electric guns are only good at short ranges.

hmm..good point.