From Sunbow's G.I. Joe cartoon, we have "The Viper Is Coming". Which is 20 minutes of dreadful setup for the horrible pun: the "Viper" in question is a foreignese-accented "Vindow Viper".
Aside from the obvious Punny Name of Gravity Falls, there's also the episodes "Tourist Trapped", "Headhunters", "The Hand That Rocks the Mabel", "Double Dipper", "Irrational Treasure", "Little Dipper", "Carpet Diem", and "The Land Before Swine". And that's just the first season...
Hanna-Barbera's version of The Little Rascals has "Yachtsa' Luck" ("lots of luck"), "Porky-O and Julie-Et" (Romeo and Juliet), "All the Loot That's Fit to Print" ("All the news that's fit to print", slogan of The New York Times), "Alfalfa's Athlete's Feat" ("athlete's foot") and "Wash and Werewolf" ("wash and wear").
Same for Road Runner shorts, which usually have titles that're puns involving either the Road Runner's superspeed (or uttering of "Beep! Beep!") or Wile E. Coyote's tendency to get maimed (Fast and Furry-ous, Zoom At the Top, Wild About Hurry, To Beep or Not To Beep, Gee Whiz-z-z-z-z-z-z, Boulder Wham!, Scrambled Aches).
My Little Pony: Friendship Is Magic has many of these: "The Stare Master" (a pun on the StairMaster exercise device), "Griffon The Brush-Off" (given the brush-off), "Owl's Well That Ends Well" (all's well that ends well), "Lesson Zero" (less than zero), "Magical Mystery Cure" (Magical Mystery Tour), "The Ticket Master" (Ticketmaster), "Boast Busters" (Ghostbusters), "Look Before You Sleep" (look before you leap), "Feeling Pinkie Keen" (feeling peachy keen), "A Friend in Deed" (a friend indeed), "Castle Mane-ia" (Castlevania), "Filli Vanilli" (Milli Vanilli), "Secret of My Excess" (The Secret of My Success), "Bloom & Gloom" (gloom and doom), and "Tanks for the Memories" (thanks for the memories).
Pound Puppies (2010) tends to use these fairly often. Examples include "Prince and the Pupper", "Mutternal Instincts", and, perhaps slightly less groan-worthy, the Halloween Episode "Nightmare on Pound Street".
The king of Western animation pun-titles is likely the Jay Ward shows, particularly Rocky and Bullwinkle. Each R&B story ended in a cliffhanger ending, with the narrator giving two possible episode titles, both of them usually puns. Example (when Rocky's strapped to a runaway missile): "'The Squirrel Next Door', or 'High, Neighbor'!"
Especially in later seasons, most of The Simpsons episode titles are puns such as "Mobile Homer", "Moaning Lisa", or "The Bart of War". The Mona Lisa, in fact, is one of the most frequent target of parodied episode titles; there have been at least three episodes whose titles use that pun, while the others are a more diverse - the only other recurring theme is "<member of the Simpson family> vs. <plot point>".
The burgers of the day in Bob's Burgers often uses punny names for the Burger Of The Day, usually referencing pop culture: for example, one burger was called "I've Created A Munster", a reference to a famous line in Frankenstein and another was called the "She's A Super Leek" burger, a pun on Rick James' hit song "Super Freak".
Paw Patrol uses one right in the title that is a Bilingual Bonus: the English word "patrol" comes from the french word "patrouiller", meaning "watch or guard something in a certain place". In Classic French, this word was "patouiller", which came from the word "pate", meaning "paw".