Here’s a few more scenes that I remembered:
Adventure Time: Finn and Jake gain weight from too much ice cream in one episode, and the reason why a character in another episode became a ghost was because he ate too much liquid cheese and exploded.
Crash Bandicoot 2 and 3: Crash swells up through beestings and pufferfishes.
We Bare Bears: Grizz gains weight as part of his hibernation process (as all red-blooded American bears do).
RWBY Chibi: Nora gain weight by eating Yang’s cake in one episode, eating pancakes laid out as a trap in another episode, and stealing cookies from a cookie jar in yet another.
Hero 108: Mystique Sonia gains weight in one episode.
My Life As A Teenage Robot: Jenny puffs up as she overloads with energy in one episode, while another has her bulge when rats take over her body. Tuck gains weight in the Christmas special, while he inflates in another episode.
Duke Nukem Forever: Two girls that Duke sights meet an explosive fate at one point.
Freaky Stories: A model gains weight after water mixes with some pills she swallowed.
Stay Tooned!: This obscure 1996 PC title features some weight gain for one of the characters in a restaurant and another in the player’s kitchen.
Johnny Bravo: Never wake Johnny up, or suffer the wrath of an air horn in your mouth. Also, Uber Mass does a body good.
Codename: Kids Next Door: Most of Sector V gets fattened up by an elderly villain.
Breath of Fire: A woman becomes fat due to literal “inner demons”.
Captain Rainbow: Little Mac, prior to his true Wii debut, has gained weight in the Japan-only Wii title.
Rayman 2: The Great Escape: Rayman gains weight in the bad ending.
Rayman Arena: Globox puffs up during the opening sequence.
Rayman Origins & Rayman Legends: The characters inflate when they lose a life.
Angry Birds series: Bubbles’ ability puffs him up, and is even shown in the animated movie.
Bratz: The antagonist of one of the CGI movies inflates after eating a burger in one of the main characters’ nightmares.
Tengai Makyou: The Japan-exclusive Saturn game contains a weight gain-themed chapter.
Pokemon games: Implied in the Full Incense’s description.
Yo-Kai Watch: Implied in the original Japanese version’s Hungramps and Whuzzhat shorts (as opposed to the English dub where Katie “looks terrible”).
Earthworm Jim: Happens to Peter and Queen Slug-for-a-Butt in one episode, and everyone that Professor Monkey-for-a-Head hits in the opening of another episode.
Super Mario Galaxy 1 & 2: Hungry Lumas become fat and full if fed enough.
Scooby-Doo series: Happens to Scooby and Shaggy frequently in the direct-to-TV movies and in one episode of Mystery Incorporated.
WarioWare: Twisted!: Happens to Wario in one of Wario-Man’s microgames.
The Legend of Zelda: A Link Between Worlds: Oren’s fate before you recover her Smooth Stone…
Zwei II: The characters can gain weight after obtaining a Scale.
And those are the instances I know so far… I’ll find more later.