Being honest, the second season episodes in general tend to be the weakest plot-wise. As if there is a rule that the quality of the animation is inversely proportional to the quality of the plot.
Anyway...
I agree with Kooshmeister that Razor's Edge is a very weak episode: the Dark Kat plan was good, but there are so many plot holes like the hospital "big conspiracy" thing or how Dark Kat knew that Razor would be the most affected by the fake incident that make that when you think about it, the episode doesn't make much sense.
But my vote goes to "The Dark Side of the SWAT Kats". As with the previous case, the idea is good, but the execution? Let's see, let's start with the premise that our protagonists go to a parallel universe because... because a beam hits Razor's Dimensional Radar.
Once in the parallel universe, we know nothing about why things are the way they are. Or why everyone is such an idiot that they don't get the differences between the two groups of Swat Kats. Hello... One pair of them have skulls on their helmets and dirty green-toned fur, and the other doesn't! Are they blind or what?

And how come the Feral in that universe captures the Swat Kats and doesn't unmask them? Or does he already know who they are and doesn't bother? And if he knows who they are, why doesn't he arrest them? Their base is still the hangar under the Salvage Yard.
That also raises the question in my mind, if that Dark Kat knows about the hangar, doesn't the one in the standard universe know about it too.
And the ending: one flash and they're back home. Either those two particular universes are connected, or they got TOO lucky instead of ending up in a universe with, I don't know... humans or reptilians. Now that the concept of the Multiverse is much more developed, it's amazing to me that they went back to their own universe so easily.
Anyway, sorry if I went on too long.