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.
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 Wrath of Con, when Splendid tries to suffocate the fire, it seems like he is going to eat everybody.
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.