The Bone characters in Bone are usually half dressed: Fone usually wears boots or nothing at all; Phoney wears a t-shirt with a star, and Smiley wears a vest (yet is embarrassed to be seen naked). Whatever the Bones are, however... eh, let's just say they qualify as "mammals" and leave it at that.
The Fox and The Crow. While the Crow sports only a bowler hat, Fauntleroy Fox wears a white collar, a blue bowtie, blue trousers and yellow gloves. He also has a matching straw hat when on the town.
Sam & Max: Freelance Police is an interesting example. Sam is fully clothed at all times (but goes barefoot) while Max is totally naked. A few jokes have been made about this, such as where Max keeps his gun (for the record, it's none of your damned business).
In the original comic books, Howard the Duck was a Donald lookalike, lack of trousers and all. However, the George Lucas film version wore pants.
At some point, Disney actually threatened legal action against the likeness of Howard the Duck; Marvel comics responded by having all future depictions of Howard appear wearing pants.
A story in the HTD black and white magazine contained a Lampshade Hanging with a twist of Take That, as a failed animator turned haberdasher forces Howard to start wearing pants. The guy let him keep his human girlfriend, though.
Lampshaded by Howard at least once. "My lawyers tell me I have always been wearing these pants."
There was an earlier story where Howard's enemy Doctor Bong transformed Howard into a human. The funniest part was seeing Howard brooding while sitting on a bed, his bare human butt clearly visible and his coat coming down to mid-rib level.
Interestingly, in Marvel Zombies Vs. Evil Dead, if you didn't know better you'd swear someone took the pupils out of Donald Duck's eyes. The Zombie Howard has white feathers (as opposed to yellow) and wasn't wearing pants.
Speaking of Marvel Zombies, it appears "My lawyers tell me I've always worn pants" is a Running Gag these days - he gives the line to Jackie when she questions his existence in Marvel Zombies 5.
Swedish children's comic Bamse has an interesting case of this, as the older the character's design is the more "nude" they tend to be. Most characters wear some form of clothing, but the amount varies from a simply bow-tie to full clothes. One exception, Wolf, remains completely naked but that's probably due to the Grandfather Clause. Skalman walks around naked half the time too, since his only article of clothing is a hat, and he generally only wears it outdoors.
Lampshaded in one comic between a Sultan and Lille Skutt, after Lille Skutt is accused of being a spy.
Sultan: A spy you said? Maybe. He doesn't look like us and he is oddly dressed as well. Lille Skutt: Are all of you crazy? First my friends was captured by the knights. They thought we were oddly dressed. And now YOU think I'm oddly dressed, even though I'm not wearing any clothes at all!!! (beat) Lille Skutt: Except for my bowtie of course.
Ink Pen plays with this slightly with its various Animated Animal Actors Hamhock and Bixby are completely buff while Ralston Rabbit only wears a bowtie and white gloves and is considered indecent without them. Fritz on the other hand is so uptight that he wears a white shirt and tie with black pants every single day. This was a problem when he worked as a stunt double for other cartoon dogs like Marmaduke or Scooby-Doo were he would wear a furry dog suit because he refused to do "nude scenes".
Played with in one Calvin and Hobbes strip, which has Hobbes dressing up as Calvin in the hope that Calvin's mum would mistake Hobbes for Calvin. It doesn't work, which according to Calvin is because Hobbes didn't put on any pants.
In comics and picture books based on The Sooty Show, Sooty usually wears red shorts with braces. (He doesn't in the show itself.)
This trope is mocked in The Beano Annual 2009 when the Nibblers (an old 1970s strip about a group of mice) meet the Ratz (a 2000s strip about a group of rats).
Evolved over the course of Archie Comic's Sonic the Hedgehog. Early on, most characters wore partial clothing ranging from nearly fully dressed (Antoine only lacks pants) to nothing but shoes (Sonic, of course). Over time, more characters were added and often featured with more complete outfits.
This can lead to some jarring comparisons if a reader starts the series late. A long-term reader won't find Sonic in just shoes odd next to say, Mina Mongoose, who wears a full set of clothes because Sonic has just always been that way. To a new reader, it looks like half the cast are rather... exhibitionist.
The with the soft reboot, many characters are starting to shift towards the current Sega look with females donning full sets of clothing and males with gloves and shoes with a few extra pieces to set them apart.
Olivier Bommel in Tom Poes wears nothing but a coat, no pants.