[Scourge of Ages]

I kept about 1 bank of EMPs for almost every bomber defense mission I flew where they were available. Just one EMP into the middle of a bomber formation would keep them from launching bombs pretty much long enough for you to close to optimal range and just shred them with your main guns. And all with just one missile instead of 6-8 trebuchets.
And if those bombers did happen to already launch bombs, EMP gives you a much better chance to knock them out.

I acidentally marked D-missile as well on the survey. I apologize, I never used that either. Blob turrets in FS1 never seemed like any sort of threat, unless you're flying a bomber. I think D-missiles in FS2 would wreck the fear that beams and flak give you, and would keep you from inventing tactics to take out those turrets.

[Androgeos Exeunt]

ST:R has this one annoying mission involving a Karnak called the Egyptos. You're supposed to protect it with EMP missiles.

[Thaeris]

...Ummm...

That's a red-alert mission, is it not? I'm pretty sure they don't give you the EMP missile, either.