Oh there are some definate diamonds in there. There is just a dip in quality when compared to first 2 seasons. The season that suffered the most was the final season, but even that one has a pretty nice diamond. Just because there was a dip in quality doesn't mean the series wasn't still entertaining. Since you made through the best of the series I don't think you will have a problem getting through the rest, but here are some episodes not to skip.
Season 3
It's a Jungle Out There
The Boogyman is Back
The Grundle
The Copycat
Halloween 2 1/2
Sticky Business
The Two Faces of Slimer. ( I just love it when Peter gets slimed and this one is heavy on that.)
Season 4
Short Stuff
Flip Side
Poultrygeist (This is a silly episode, but I have a real soft spot for it.)
Standing Room Only
Robo Buster
Season 4 is pretty short so It's easy to get through.
Season 5
Loose Screws
The Ghostmaster
If I were a Witch Man
Somethings Going Around
Jailbusters (This one has some very choppy animation and you'll notice that the episode is slowed down to fit the hour format of the show at the time, but I enjoy it when they go into the spirit world.)
Ghostbusters Live From Al Capone's Tomb
Partners In Slime
Elementary My Dear Winston. (This is another one that has some odd animation and timing issues, but still fun.)
The Halloween Door (This one aired during prime time so they were able to get away with things they couldn't do on Saturday Mornings. It also has some of the best animation in the series. Definately the best episode to air after Studio Interference.)
Season 6 and 7
Janine You've Changed
The Slob
Not Now Slimer
Skip Deja Boo it's a Slimer focused episode and it is a clip show of better episodes. Unless you really enjoy Slimer and Dweeb.
I hope you enjoy the rest of the series. Definately don't miss the episodes above.