Rats (and a Gary-rat with a Fly) in "Stingstress"
"Superfail". Don't know if it strictly counts, but it has a rat's butt.
Another instance of a Gary-rat and Fly, in "Uh Oh It's Magic"
Dead gutter rat in "Sticky Discharge"
Twins riding a rat in "Special Needs"
A Twin transforming a rat in "The Trouble with Triples"
Lunch ladies killing a rat in "Nightshift"
THE Rat in "Planet Radio"
Unlucky rat in "Burn Stoolie Burn"
Season 3’s bunch of rats. The only episode that doesn’t seem to have them would be “Oedipus Mess”, unless an army of Jacknife could be seen as some sort of vermin.