The male animatronic characters in Dinosaurs didn't wear pants. Females wore dresses sometimes, but if they were dressed as if they would wear pants they went bottomless too. This was pointed out one episode in which they showed Earl wearing a pair of pants because of censorship happening all over the show.
This was lampshaded, during the Very Special Episode no less, when Robbie, while high on "happy plant", collapsed in a fit of hilarity upon realizing that none of them wore pants.
Who can forget Humphrey B. Bear? The strange thing about any discussion involving him, of course is that people point out his lack of pants. Never mind that he's a bear wearing a (rather stylish) boater and waistcoat - which it has to be said, is not something bears are known for. Oh no. A bear not wearing pants? Disgraceful!
Mystery Science Theater 3000 once addressed this phenomenon during a '50s educational short in which a Porky Pig figurine could be briefly glimpsed atop a desk. Tom Servo: "Get Porky some pants!"
This was sometimes done with the robots as well. In the episode featuringGirl in Gold Boots, Crow becomes a stripper (imitating the film's main character), dances around in a little gold bikini, and then proceeds to remove it. Mike is completely disgusted, but Servo points out how illogical this reaction is considering that Crow generally wears nothing at all.
The monkey's the only cookie animal that gets to wear clothes, you know that? ... So, I'm wondering, do the other cookie animals feel sorta ripped? Like, is the hippo going, "Hey, man, where are my pants? I have my hippo dignity!" And you know the monkey's just, "I mock you with my monkey pants!" And there's a big coup in the zoo.
The Muppets: Kermit usually wears nothing but his collar, and will cover himself up if it's taken off. Fozzie Bear only wears a hat and tie, which was once the basis for one of his routines. ("Good grief, the comedian's a bear!" "No he's a-not! He's a-wearin' a neck-a-tie!") Rizzo the Rat wears a jacket and hat but no pants, as does Pepe the Prawn. Of course, most of them are never seen from the waist down, so it's usually a moot point.
In The Great Muppet Caper Fozzie and Kermit play twins. Nobody recognizes them as such until Fozzie removes his hat. Later on Kermit is sitting alone and a passerby mistakes him for a bear. Someone else corrects him; "Bears wear hats."
Alien Gordon Shumway from ALF wore shirts on occasion. He's usually not shown from the waist down, but this trope is considered plausible based on his wardrobe in the animated series of the same name.
The three adult animals in Odisea Burbujas Patas Verdes (a toad), Mafafa (a lizard) and Pistachón (a bee). Patas Verdes and Pistachón wear no pants at all, but they do have hats and clothes over the waists. Mafafa wears a dress as she's the only female, but nothing else.