Well but here's the thing: The show has done a LOT of jokes over the years about dark subject matter. Yet I still laugh at them. Like all the quick gags where someone is maimed or killed. (Remember the unfortunate man who was struck by all sorts of construction tools in "King Size Homer"?)
The difference with "Homer's Enemy" is the whole overtone of the episode, save for the light-hearted Bart/Milhouse stuff, is dark. There's a sense of hate, contempt, and dread in the air, thanks to Grimes. Even if you were to take out the ending where Grimes accidentally kills himself (death is a popular dark comedy subject, but it only amounts to the last minute of the show), I would still call this episode dark, just from the way it's executed.
So I guess what I'm saying is, it's not that there are many jokes in the episode that I know I shouldn't laugh at but do (aside from the ending, which I still have mixed feelings about), but that the more serious tone of it all makes the comedy not as light-hearted, madcap and zany as it usually is.
As I'm 100% sure this was a facetious remark and you're not confused, I have to ask what the point of this post was, other than to bash the later seasons (which is not only off-topic but beating a dead horse).