Bizarro Episode: Some of the shorts not created by Jones due to different aesthetics and heavier breaks in formula. "The Solid Tin Coyote", "Sugar and Spies" and "The Wizzard Of Ow" are particularly unique in the fact that, rather than being an episodic compilation of interchangeable schemes, Wile sticks to refining one consistent and unusual gimmick the entire short.
Death of the Author: While Chuck Jones' "Rules" of how the series was written is somewhat well known, his contemporary Friz Freleng considered his account of the series rules apocryphal, saying he made up the rules long after the original shorts were finished. Considering how often some of the "rules" were broken in the original shorts, there may be some grain of truth in that. Writer Mike Maltese also confirmed that there were no "rules" when they made the original shorts either.
Epileptic Trees: Cracked presents the theory that Wile E. Coyote has a clone army, and the coyote who talks is the real one. It's surprisingly plausible. Someone left an equally plausible comment suggesting that the Road Runner is either a clone himself or in cahoots with the original Coyote, acting as bait/an incentive for the clones to test ACME products.
Fanon Discontinuity: Rudy Larriva's eleven Road Runner shorts (and, arguably, Robert McKimson's two efforts along with the Sylvester/Speedy crossover directed by Friz Freleng) tend to be considered part of WB's Dork Age.
Memetic Mutation: Still images or GIF's of a horrified Wile E.Coyote holding a sign saying "Stop! In the name of humanity!", has been used in comment sections to plead people they're responding to, to calm down with percieved inflammatory or squicky comments.