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."
In Nintendo's social simulator video game Animal Crossing, most animals wear shirts 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, 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 realising and commenting on the fact they don't wear pants.
Sheep villagers wear shirts as scarves instead, making them accessory-wearing instead.
The Donkey Kong family is another pretty interesting example. The big guy himself wears nothing but a tie, Diddy settles for a shirt and hat, but some of the other members of the family, such as the other 3 main character in Donkey Kong 64 are more or less fully clothed.
Even some of the Kremlings that Donkey Kong fights wear pants and no shirt (although that may simply tie into the pirate motif that K. Rool's empire inconsistently follows).
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. Additionally, Bubsy's best friend/unwilling sidekick Arnold the Armadillo is completely nude.
Bowser never wears clothing except for one occasion in Super Paper Mario where he is seen in a white tuxedo briefly, minus the pants.
The official artwork of the shell-less Koopa Troopas for Super Mario 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.
Wart from Super Mario Bros. 2 wears a royal robe and a crown, but doesn't wear a shirt or 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.
Rareware loves this trope.
Banjo 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)
Several characters in the Donkey Kong Country series, such as Diddy, Dixie, and Chunky, wear shirts (and in the former two's case, hats as well) but no pants.
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.
The main characters of Super Monkey Ball are of both types: Aiai and Gongon are of the pantless variety, and Baby and Meemee of the Shirtless variety.
Chuck Rock has every animal enemy be naturally naked, but the final boss is an anthropomorphic dinosaur wearing a crown, boxing gloves, and underwear.
Most of the Funny Animal characters in the Sonic the Hedgehog series wear no clothing at all except for their shoes and gloves. Only female characters like Amy, Cream, Rouge, and Blaze are fully clothed.