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"Operation: Rabbit", where he tried to chase Bugs Bunny — the rare cartoon where he had lines, and he turned out to be a Wicked CulturedSmug Snake with a massive superiority complex ("Wile E. Coyote.... Suuuuper Geniusssss!"). Naturally, this made his total annihilation even funnier than usual, culminating in an incident involving a shack full of nitroglycerin-filled carrots and an oncoming train.
A bridge contracts as the Road Runner passes over it. Only one of the uprooted cactus plants fails to clear the bridge. The Coyote, of course, falls into the chasm underneath the bridge. The cactus follows, and guess where it lands. Cue the Pain-Powered Leap and Eat The Camera scream.
Put the two together, and what do you get? "Hare Breadth Hurry", a Road-Runner cartoon where Bugs Bunny fills in for our favorite speedster. What follows is a hilarious mix of both kinds of cartoon.
"Zoom and Bored", where Wile E Coyote had built an enormously complicated contraption to drop a bomb onto the Roadrunner. They spend about three minutes just panning up the thing. When we finally get to Wile E Coyote at the top, he lights the bomb... and it instantly blows up in his face.
A similarly CMOF contraption showed up in the finale of "Hook, Line and Stinker", and ended up pounding Coyote into the ground with his own cannonball.
This was referenced in Ian Frazier's short story, Coyote v. Acme. Which would be a Crowning Moment of Funny if it weren't just the plaintiff's opening statement of a civil suit against Acme...
Also from "Zoom and Bored", the very end. Wile E. Coyote is catching his wheezing breath on the clifftop after getting dragged through the desert and then hit by a train. Enter Roadrunner, who displays a sign reading "I just don't have the heart".
A taut cable from the top of a bluff to the road below, and a helmet with a caster bolted on top...
A hot air balloon with a garbage wagon gondola with an anvil tied on...and no consideration of what would happen when the anvil was released...
Let's not forget the scene where Coyote is so relieved at just having avoided falling off a cliff, that he strides off in the opposite direction... you guessed it... straight over another cliff.
Coyote gets into a hot air balloon with well over a dozen dynamite darts. Said darts are released and proceed to torment the Coyote for the rest of the short, including, but not limited to, blowing up the previously mentioned balloon right off the bat, blowing up the Coyote's parachute for when the balloon failed not ten seconds later, plugging the Coyote's rifle, and breaking a skinny cliff.
The chase Wile E. and Roadrunner have in an underground mine. They're represented from afar as two dots, one of which is pursuing the other. The two dots go hell for leather around the mine, so fast that at first even the viewers barely realise when the actual chase stops. It stops because Roadrunner has stepped into another passage just out of sight, leaving the Coyote to run madly round and round the same square mine passage wondering where the hell he's gone. This goes on long enough for the audience to figure it out and laugh themselves stupid. And the way Wile E. comes screeching to a halt when he spots Roadrunner's hiding place is priceless.
At the very end of "Soup or Sonic", the Coyote chases the Roadrunner through a pipe that gets smaller and smaller, until they come out the other end, only a few inches tall. So they go back through the pipe... but only the Roadrunner returns to regular size. The tiny Coyote triumphantly throws both arms around the Roadrunner's ankle, pulls out knife and fork, looks up at the Roadrunner now towering over him... After a moment of stunned indecision, he holds up signs reading, "Okay, wise guys, you always wanted me to catch him — now what do I do?"
Gotta love incidents where there's...more than a little play in the fuses. From the Coyote striking a match, lighting the fuse, and the fuse burns down completely before he can turn around, making the device explode, or him touching the flame to the fuse and the explosives goes off right then and there, period.
One short has Wile E. buy an industrial strength rubber band and construct a slingshot, in the hope that it will give him enough speed to catch the Roadrunner. Roadrunner runs by, Wile E. cuts the line and releases the rubber band, and... nothing happens. It stay taught, much to his confusion, so he gets out from the rubber band and checks to see what's wrong, including sticking his head into the rubber band to see if there's anything beneath it that has it snagged. Then the rubber band decides to release, slamming Coyote into the ground a few yards away.
The ending of "Scrambled Aches"; Wile E. builds a giant steamroller, but it rolls away from him. The out of control steamroller chases the Road Runner into a detour ("In case of steamroller, use detour!"), which the Road Runner runs into...right into a cannon. Wile E. jumps behind it and lights the fuse, but the cannon doesn't fire, so Wile E. looks into it. Suddenly, the Road Runner comes flying out on top of the cannon ball, and just when you think it's over, suddenly the steamroller appears, running towards Wile E. The fact that the steamroller is GONE for a good chunk of this plan, and then just shows up at the end out of the blue, is pretty much the funniest thing ever.
"There They Go-Go-Go!" The Coyote is rolling what looks like a nautical steering wheel, complete with spokes of dynamite, toward a slope. He lights all eight dynamite sticks and launches the wheel... and off goes the wheel, but not the dynamite. Kaboom.