My single worst encounter (with an honourable mention to facing down Standoff's Vatari in a Stiletto, which is not eligible for the award but is the only fight in which I happily accept the enemy's decision to retreat) with Kilrathi forces isn't any of those - it's the Dralthi horde you encounter in WC3's Alcor System - on Nightmare, they don't need a missile lock to swarm you with ImRecs, they're very hard to follow, and your Arrow is fragile.
Overall, assuming that I should be comparing WC3 fighters to those in earlier games based on default difficulty rather than Nightmare, I think the Hhriss wins out just about, though more through its sheer endurance than anything else.