The end of Autopsy Turvy (Double Whammy, part 2.) After revealing the epic battle between the normal and evil Flippys is really just Flippy fighting with himselfthe entire time, both sides, badly battered, pull out at least a dozen copies of themselves each... and then they go all out against each other.
The entire second half of that episode counts, too. Turns out Good Flippy is every bit as Bad Ass as his evil side.
Flippy's Evil Side fighting Tiger General in Operation: Tiger Bomb. The General is the only character in the entire franchise to put up a tough fight against Fliqpy, and actually came pretty close to killing him.
Flaky gathering all her courage and stabbing Flippy in the eye, trying to kill him on purpose. The only character in the whole show who actually realizes that Flippy is insane and horrifyingly dangerous. Though, since she did it to the innocent and helpful version of Flippy, this earns her a Karmic Death via airbag.
In By the Seat of Your Pants, Lumpy manages to outsmart Fliqpy. To make things even better, he does it while panicking.
Lumpy managed to kick Zombie!Flippy's ass earlier in the Halloween special "Remains to Be Seen". After his hand gets bitten off, Lumpy attempts to replace it with a chainsaw, but gets a leaf blower instead. Nevertheless, he manages to inflate Flippy's brain and draw in the other zombies, killing them in the ensuing explosion when Zombie!Toothy pops the brain while trying to eat it.
In general, it's awesome to see Evil Flippy get killed for a change.
In Doggone It Lumpy faces off with a giant squid with only a mousetrap. And wins.
Lifty & Shifty having the upper hand on Splendid in Gem's the Breaks. Special points given here because they're the only two characters that give Splendid a hard time (besides Splendont, that is). Also, extra points to this episode for breaking Splendid's immunity, and having him actually die (though the explosion in Class Act killed Splendid as well).
In Wrath of Con, when Splendid lifts up the chunk of the building, the second time this is shown, it Art Shifts to a painted style. Not only that, he is given pectoral muscles and an Exposed Animal Bellybutton. Unlike other Art Shifts, this one is still.
In "Easy for you to Sleigh", Lifty & Shifty go around on Christmas stealing from people and inadvertently killing Pop and Cub by blocking the chimney with their tree (though Pop didn't help matters by disabling the smoke detector). Then they rob Flippy, and wake him up after having tied him up. He proceeds to flip out and kill both of them, removing one of their faces with a Christmas Cookie.