The Dark Crystal actually has two short-ish races, the smallish Gelfling and the even smaller "Pod People" (who look kind of like potatoes and live in big seed pods). Then again, there are no human characters, and everyone else is either a reptilian or a something like a very tall angel, so the scale isn't totally clear.
The Little People who work for Mr. Tiny in the Cirque Du Freak series. While the small, blue-hooded, (mostly) mute Little People are minor characters in the beginning, one of them, Harkat Mulds, quickly becomes a major character.
Mythology and Folklore
Many mythical depictions of elves were like this (Santa's elves, for instance), until Tolkien repopularized the 'tall' elves of ancient myth into modern fantasy.
The Dragonlance setting introduced the Kender, which served as a different take on the Little People at the time (even if it was considered the Scrappy race due to annoying players playing up the kender's natural curiosity, fearlessness, and kleptomania). This helped evolve the Halfling in later editions past "hobbits with the serial numbers filed off".
The Dwarves of the D&D settings were short, but they don't fit the cute or childlike part of the trope. They tend to be characterized as dour, tough, and warlike, and they tend to make good fighter characters.
The Ratlings of Warhammer 40,000, though they don't have much presence in the game besides being specialist snipers for the Imperial Guard.
Also, before their tragic death by Tyranid, the fabled Squats.
The Lilties in Final Fantasy Crystal Chronicles are a very small and cute race. They're also super-adorable (and can crossbreed with people). Oh, and they used to be The Empire and can be extremely hardy and gruff, are incredibly strong for their size, can forge some mean weaponry, and can hold a grudge with the best of dwarves. Do not cross a Lilty of you know what's good for you.
The yordles from League of Legends are short humanoids who come in a number of variants; some are furry and animal-like, such as Teemo and Rumble, while others are more like small humans, such as Corki and Poppy.
The Firbits in Dark Chronicle are half the size of the protagonists, addicted to grape juice, and their eyes are always covered with hair or glasses. While relatively mature, they have a habit of lapsing into childish responses, not unlike the Moon Folk from the previous game.
Everquest II has a vast array of little folks for players to take on, including five races (Fae, Arasai, Froglok, Gnome and Ratonga) who are half the height of humans or less!
Ben 10 has Galvans, Grey Matter's species. Ditto and Echo Echo also are really small, but not as small as Grey Matter, and they share the duplication gimmick. In a bit of a subversion, Galvans are the setting's High Men, ruling over a vast technological empire and being responsible for building most of the cool Imported Alien Phlebotinum, including one of the races Ben can turn into (Upgrade) and the Omnitrix itself.