Lampshaded in El Goonish Shive, though it's only used partially and only for some of the animal-people. The "brothers" of Grace, animalistic shape-shifters, are Guineas (a guinea pig), Hedge (a hedgehog) and Vlad (a bat... sorta). The kicker is when Elliot, temporarily transformed into a cat-person, is caught and interrogated by Damien.
Damien: Now, what is your name? Elliot: Um, well, what with me being a cat and all... Cat? Damien: All of you animal-people have horrible names.
A character in Sinfest is a dog named Pooch. Monique lampshades the absurdity, furiously asking Pooch's owner if he'd name her "Girl".
The robot from Zap!'s real name is XR-743-9Q. Zap can't remember it, so he redubs him to Robot.
In Rusty and Co., the main characters are a mimic named Mimic (actually Boxford), a gelatinous cube named Gelatinous Cube, and a rust monster named Rusty. When Mimic's real name is mentioned, and he lampshades how silly it would be for him to actually be named "Mimic", Kris points out that he knew a human named Manny and a guy named Guy, which he considers equivalent.
A non-animal version comes up in Schlock Mercenary, when Tagon asks Petey what the local inhabitants — whose water-covered planet they're orbiting — call their world, it comes out as "Wet". When Tagon comments that this isn't very imaginative, Petey replies that they compare favourably to the natives of "Earth".
In Trying Human, Hue had a pet dog (that was accidentally abducted along with a pair of hippies). He never calls his pet anything else but Dog.
Annie in Gunnerkrigg Court builds a robot in the very first chapter and starts calling him Robot. He does have a proper name, revealed later on, but the main characters keep calling him Robot (which can get somewhat confusing since there's a lot of other robots in the story).
White Dark Life: At first a name like Entegra Whidoe seems more like a case of Meaningful Name since the character is a black widow. But remove the first "E" and "T" from her first name turns it into Negra(Black) Widow.
The endlessly creative Kleya Smith created a Cat Girl character for the Game, naming her Kat. Several other characters imply that she's not the first one to use that particular combination either.