Primarily, as Kanga said, cruise disruptors will cause your opponent's engines to "kick back on" if he's using engine kill.
Oftentimes, larger ships such as gunboats or cruisers will engine kill and then turn towards you while they're still moving away - this lets them overcome the disadvantage of having a much slower turn rate when fighting against more manuverable enemies. If you cruise disrupt them when they try this little tactic, it will usually cause copious amounts of swearing and desk-banging as the pilot tries helplessly to keep you in his crosshairs.
Additionally, cruise disruptors can be used to prematurely detonate most mines, missiles, and torpedoes (no longer works on nova torpedoes, though, so bear that in mind). Train cruise disruptors work great for this as they have a very large radius, making it easier to force detonate either your mines/missiles or those of your opponent - but mosquito disruptors work nearly as well and have less tendency to piss off nearby NPC's.
If your opponent is spamming mines, typically spamming cruise disruptors back at him will cause his mines to blow up right as they leave his ship, and he'll end up killing himself. Same thing with missiles, if you can time your disruptor to hit right after a target launches missiles at you.