In Nintendo's social simulator video game Animal Crossing, most animals wear shirts (sheeps wear scarves) but go without pants. (Humans do wear shorts.) Different species wear shirts of different lengths, and male characters of some species wear relatively long shirts (except in New Leaf) , which some players confuse with cross-dressing. But interestingly enough, clothes are one size fits all: take a shirt off one character and put it on another character, and it magically fits. Somewhat hilariously and scarily lampshaded in one animal-to-animal conversation in Wild World, where jock archtypes comment to nice archtypes that he split his pants doing squats. The nice animal begins to find this hilarious just before realizing and commenting on the fact they don't wear pants. (Weirdly enough, both Kid Cat and Snake can say this conversation, despite both of them wearing pants)
In Armello none of the Heroes wear pants. And only about half of them of either gender have skirts (mostly armored).
Katt/Rinpoo from Breath of Fire II walks around the whole time wearing a purple top and leggings, but no pants, with no visible reaction from anyone on her state of...erm, undress. However, the bottom half of her body has fur while her top half has normal "human" skin.
Bubsy wore a shirt and no pants. Various promotional materials for the game made a point of mentioning this. Bubsy's nephew Terrence, introduced in the second game and also appearing in the animated adaptation of the game, also had the pantsless look.
Chuck Rock has every animal enemy be naturally naked, but the final boss is an anthropomorphic dinosaur wearing a crown, boxing gloves, and underwear.
Crash and Crunch Bandicoot, and Dingodile all have shoes, gloves and pants, but lack a shirt. Ripper Roo wears a straightjacket, but no pants.
From the Donkey Kong series, Diddy Kong, Dixie Kong, Cranky Kong, and Chunky Kong all wear shirts, but no pants. Swanky Kong was also this in Donkey Kong Country 2, but he later switched to Fully Dressed Cartoon Animal in Donkey Kong Country 3. The Kritters in Donkey Kong 64 and the Mario Strikers games wear some form of top-wear, but no pants. Some of the Kremlings (Most noticably the Kritters ever since their redesign) that Donkey Kong fights wear pants and no shirt (possibly to tie into the pirate motif that K. Rool's empire inconsistently follows).
Some of the beast tribes in Final Fantasy XIV wear some form of clothing that covers up their genitals, but they are naked for the most part; the lizardmen Amalj'aa wear a large metal codpiece on their crotch and wear various forms of jewelry on their necks and arms. The Ixal, a bird-man race, wear what is basically a jockstrap and sometimes straps on their chest. The Sahagin are fish-like creatures that wear a mixture of a codpiece and loincloth while wearing various jewelry elsewhere. The Vanu Vanu are a tubby are a gryphon-like race that only wear a tribal loincloth and/or a sash across their chest. The Gnath are a race of insects and only wear a scarf/cape. The Kobolds are the only beast tribe that are fully clothed with a helmet, a shirt, and pants, but no shoes.
Five Nights at Freddy's has the 'pants only' form of the trope with Foxy, whose torn brown pants fail to cover his bare metal legs. This makes him the most dressed of the killer animatronics—the rest only wear accessories.
Not necessarily an animal example, but when Sol Badguy turns into his 'Dragon Install' form in Guilty Gear Xrd, he wears a really short jacket, but no pants.
Several characters from the Jump Start series of CD-ROMs. Frankie Dog wears a red sweater and collar; Keisha Koala wears an art jacket, beret and sandals; Hopsalot Rabbit sports only a T-shirt; and Casey Cat has a T-shirt and backwards cap.
King Dedede's design design has him wearing a red coat, a crown, and a waistband. His current design since Kirby Super Star is debatable, as his entire body is now cream-colored instead of blue, but his design in the early games, Kirby: Right Back at Ya!, and the official artwork for Kirby: Squeak Squad clearly shows he's not wearing pants.
Daroach from Kirby: Squeak Squad wears a red trenchcoat and hat, but not pants. Storo is also pantsless, as he only wears a red sleeveless shirt and bandana.
President Haltmann from Kirby: Planet Robobot has him wearing complete business attire...except for pants.
It is unclear if the Rito in The Legend of Zelda: Breath of the Wild are wearing puffy pants or if they're actually their pelvic-feathers, but if it's the latter, then they are certainly this trope, as they wear some form of top-wear.
The Abra and Machop lines play with both variants of this trope. The entire Abra line seem to be wearing brown chest-plate armor, but also appear to be pantsless. While Machop is completely naked, its evolutions, Machoke and Machamp, seem to wear speedos (Which are actually markings) and wrestler belts.
Mega Alakazam, however, is a Barefoot Cartoon Animal, as it gains pelvic armor not too dissimilar to its chest-plate armor.
Incineroar from Pokémon Sun and Moon is supposed to be designed like this, with a wrestler mask-like head, a gray torso that resembles a wrestler tank top, and a (literally) flaming champion's belt, but its lower body is the same color as its head and arms, making it look pantsless. Given it's masculine appearance, this also makes Pokémon X & Y's Delphox a Distaff Counterpart to it, which is a feminine-looking Pokémon with a Fully-Dressed Cartoon Animal-like design, seemingly playing with the Pantsless Males, Fully-Dressed Females trope.note Though it is worth noting that both Delphox and Incineroar can be both genders. Even more noteworthy is that male Delphox are a lot more common than female ones.
Banjo from Banjo-Kazooie never wears a shirt, but is never seen without his yellow cargo shorts and blue backpack. Additionally, all his transformations keep the shorts and backpack. Yes, this is probably the only series where you will see a washing machine with shorts. Interestingly enough, his sister Tooty is fully clothed (aside from shoes), his friend Bottles wears only a vest, and his companion Kazooie wears nothing at all.
Sabrewulf (a werewolf) is a curious example in Killer Instinct because he, for some design reason, uses both of the trope main styles in his only two canonical games, he is pantless in the first game and shirtless in the second one.
Conker the Squirrel wears a blue jacket, gloves, and shoes, but no pants. This is made extremely weird in the mission where Conker must piss on fiery demons trying to burn him up: You can hear a zipping sound as if he is unzipping his pants, but he has no pants! So what the hell is he unzipping? His fur? (However, in the Xbox remake, Live and Reloaded, Conker is given pants, so the zipping sound in the pissing mission makes sense now)
In Diddy Kong Racing, Diddy Kong, Conker, Krunch, and Taj all wear some kind of shirt without any pants. Additionally, Banjo and Drumstick wear shorts and overalls respectively without a shirt.
The back-up dancers from the Frog Hop minigames in Rhythm Heaven play with both variants of the trope. In the first game, they only wear pants, but in the sequel, they gain blue sleeveless vests, but wear no pants. The lead dancer and singer wear the same pants in the first game, but they are both fully-dressed in the sequel.
The characters in the Sly Cooper series are a pastiche of cartoon Talking Animals. Most of the male characters are habitually pantsless; however, almost all the female characters have pants or a skirt with an appropriate tail-hole as needed. The exception is The Contessa from Sly 2: Band of Thieves, but she's a spider-centaur-thing with no humanoid legs.
In a behind-the-scenes unlockable in Sly 2, one developer comments that Sly is "a universe in pants-less-ness."
Elora the faun in the Spyro the Dragon series wears only a top over her human torso, with nothing but fur covering her lower half, though most other fauns either wear full dresses (female) or nothing at all (male).
The official artwork of the shell-less Koopa Troopas for Super Mario World and their appearance in Super Mario 3D World shows them with a shirt and no pants. Later on in the series, they are shown with a shirt and shorts. Clothed or not, they all wear shoes and it matches the color of their shells. However, the Paper Mario series seems to imply that shells are effectively the same as clothing for Koopas, so make of that what you will.