Not sure if we're allowed to count SM and SO, because the answer changes, but here's my take:
WC1: The Gratha. It would be the Rapier, but since that was a "special case" and not something that regularly showed up on my radar, I'm not counting it. Salthi and Dralthi were pathetic, Krant were only annoying due to their sheer numbers, and Jalthi, while dangerous, could be easily outflown and brought down if you were careful. But the Gratha wins, if only for that mission in Kurusawa.
SM1/2: The Hhriss. Not the worst fighter ever to face, but significantly more dangerous than any other cat fighter in the WC1 era. The Dralthi II is a close second, only because its incredible numbers combined with its mass drivers made big furballs a bad day.
(In general, I think WC1 had the most well-balanced array of enemy fighters...no one type stood out to me as "pathetic" or a "superfighter").
WC2: The Grikhath. Frikkin rear gun. Also, small target profile, thick armor, and you had to go after them because they were a threat to capships.
SO1/2: With all due respect to Drakhai-flown Sartha, which were nasty, let it be known for all time that I HATE GOTHRI. Gothri are evil. By the way, did I express my dislike of Gothri? (Imagine how happy I was when I got to Standoff Ep 2 and found that mission where you're dogfighting like 30 Gothri, which are just as hateworthy in Standoff as they are in SO).
For the record, I never understood what the problem was with Jalkehi. This seemed the most broken fighter in WC2...they never really posed a threat to me, blew up really easy, couldn't hit the broad side of a dreadnought, and were all around the thing I found easiest to take down. Must be the biggest discrepancy between what a fighter was supposed to be and what it was.
WC3: Vaktoth. Far and away the best craft the Cats had. It was too heavily armored and shielded for an Arrow to be comfortable against (and it had a rear gun as bad as a Grikhath). It was too fast and maneuverable to keep up with in a Thunderbolt or a Longbow, and it was evasive enough to avoid a missile or two, and tough enough to take a few missile hits, so you couldn't just lob FF's at them to get rid of them. Strangely, the best fighter against it was the Hellcat, which, as far as I can tell, is the only reason why one would knowingly choose a Hellcat in WC3.
Incidentally, does anyone else think that the Vaktoth design might have grown out of the successful Grikhath design? The Vaktoth looks kind of similar in shape, and both serve similar roles--a heavy, powerful, jump-equipped attack fighter with decent speed and maneuverability for its size, lots of firepower, and a nasty reargun.
Never had much trouble with either the Rockships or the Sorthaks--yes, they took a while to kill, but weren't all that threatening.
WC4: Leaving out the Lances (a.k.a. "Dragons"), which, as superfighters, were obviously the toughest, I would say worst fighters were whichever non-pirate fighters outnumbered you the most. The AI in WC4 was good enough so that ANY of the BW or Confed fighters, if they outnumbered you, were nasty. I would rather face two Lances than four Hellcats or Banshees.
WCP: Devil Ray, obviously, but if we're ignoring that, it would be the (blue) Manta. Morays and Skates (broken up) and Remora were no threat whatsoever, and were just killboard padding. Likeways with Rays and Lampreys. Unbroken Skates had to be tackled because they were a threat to capships, but didn't scare me in my fighter. Stingrays were bad, and Red Mantas were a bit of a threat both in a dogfight and versus capships, but blue Mantas were both tough in a dogfight, well armored, fast, maneuverable, and usually met in astounding numbers.