Yami/Atem used to remain the same size in the first manga, but then got a case of import and started getting a growth spurt like his anime counterpart after the transformation. Can be seen clearly in Yu-Gi-Oh! R.
Name a Mon that's under a couple of feet high; good chance it'll be completely adorable. Shaymin gets bonus points for not only being one of the smallest of the 649 pocket monsters, but a Legendary as well. Screw the Sky Forme, cute hedgehog is cute.
Every generation has a miniature Olympus Mon or two, like Mew, Jirachi, and Manaphy...
Joltik's the smallest of all Pokémon (10 cm/four inches), and is ridiculously cute to match.
Talking about Mons, MarineAngemon is definitely Digimon's take on Shaymin (or is it the reverse, since MarineAngemon came first?). Also, this Kapurimon◊ is one of the third-grade-equivalent students at a school in one episode of Digimon Frontier. (He's existed in other media for much longer, and it appeared briefly in Digimon Tamers.) In-Training level Digimon are almost always toothachingly cute. (But if he hits you with his tail, you will feel it.)
In the same vein, Reinforce is a lean, mean, living killer machine. Reinforce Zwei, on the other hand, is a 6-inch tall, supremely cute and flat chested. However, she still carries a large dose of ass kicking (when properly...ahem, "used", since she's still technically a living weapon). Although Zwei can "upsize" to roughly Vita's size, as mentioned in the Sound Stages and demonstrated visually in Force.
Mahou Sensei Negima! has Chibi-Setsuna, the adorable shikigami Setsuna pulls out when she has to accompany someone but needs to be somewhere else at the same time.
Aisaka Sayo also counts when she is possessing the Voodoo doll.
There are also the magic de-aging pills that allow the girls to turn themselves into lolis. Chisame in particular says that she prefers her "Chibi-Chiu" form to her normal self.
Lumiere of Kiddy Grade has the ability to create cute, miniature search subroutines. When Tweedledee sees this, she remarks on how cute they are, and creates her own version.
Medabots. Full-powered combat robots... in a three-foot tall package (well, except for that one that Ikki disabled in one episode, that qualified as a Humongous Mecha). Did I mention that Medabots are kid's toys?
In Soul Eater, Medusa possesses the body of a little girl, and twists her appearance into a copy of her original one. Uses the cuteness to her advantage in the manga when she got herself imprisoned by Shibusen (similar in the anime, but the reaction isn't quite the same). Usually looks cute in this form, but not always.
The laptop-model Persocoms in Chobits! Sumomo (aka Plum; there's a little debate as to whether or not the name should be translated) is smaller than your forearm but several times as cute as human-sized Chii. Her Cheerful Child personality adds to it, though Kotoko is also insanely cute despite her quite serious personality.
Comic books: WaRP Graphics' Elfquest had elves that were about half as high as humans. They were adorable.
Yeah, that wasn't quite the point, although the Pinis did mention in an interview that giving them large heads and eyes made audiences feel more protective toward them.
And there were also the "Tiny Toon Elves" self-parodies, drawn IIRC by some of the original Tiny Toon Adventures artists.
The extradimensional X-Men villain Mojo, in an effort to keep his world's television ratings high after their (presumed) death, created Fun Size versions of the titular mutants — the X-Babies.Hilarity Ensues when the babies prove to be less restrained than their adult counterparts.
Despite (or perhaps because of) hilarity destructively ensuing, it was apparently a ratings success, because he later brought out the Mitey 'Vengers (Fun Size Avengers) and a team of Fun SizeAge of Apocalypse villains, including the terrifying four-armed head-for-a-torso Sugar Man.
In the Series 3 finale of Doctor Who, the Master makes the Doctor look as old as he is (900 and something years old), and he turns into an adorable tiny creature. The thing that made the Doctor look cute was his huge eyes, which completely makes you look past his grey, withered skin, and bony hands.
An episode of Will and Grace made mention of the "Pocket Gay" when Will was set up on a blind date with a guy who was quite short. Jack basically described him as "all the perks of a boyfriend in convenient travel size."
Bernadette is the sweetest, cutest member of the gang in The Big Bang Theory. At under five feet she's also the shortest.
Bernadette: I've never seen you wear this dress, it's adorable!
Penny: That's because on me, it's a shirt.
While nearly all fairy species in Artemis Fowl are small at around a metre tall, pixies specifically are said to be cute, rather fragile, and similar in appearance to human children.
Team Fortress 2 gives us the mini-sentries, which are basically the standard sentries at a smaller size and significantly less firepower, with a police siren duct taped on top of it. Of course, this is lampshaded by the Engineer himself, as he sometimes calls it a "cute little gun".
Taken further with Dungeon Defenders, if purchased from Steam you also get the Engineer/Pyro/Heavy/Medic as a pet.
The Sonic the Hedgehog series is fond of using little chibi versions of the characters as icons. In Sonic the Hedgehog CD, Sonic (and Tails in the digital remake) are shrunk down into chibi forms in Metallic Madness zone.
The Downsize status ailment in the PS2 remake of Tales of Destiny does this to your characters by making them take on their tiny Super-Deformed sprites from the original version of the game.
A mob of tiny, squeaky voiced Chelsea clones is also fought in the bonus dungeon.
Girl Genius has fun with this. Played straight by the Dingbots. Inverted by the "Fun-Sized Mobile Agony and Death Dispensers" — old Heterodynes did everything very... FUN sized (they probably heard about miniaturization, but thought it's about Shrink Ray).
Tiny!Katara: Tiny Zuko! He looks so cute! Tiny!Zuko: (attempts to resume normal form) I AM NEITHER CUTE NOR TINY! Tiny!Iroh: You are pretty cute, my tiny nephew.
SpongeBob SquarePants has the Krabby Kiddie Patty which is "thirty percent cuter" than a normal krabby patty.
Chibi versions of the characters are used for gags in Totally Spies!. In one episode, Alex finds Clover adorable after she is shrunk to insect size.
Spike in My Little Pony: Friendship Is Magic is the youngest dragon we see, and is appropriately tiny. He's even smaller than the foals in the series who can also count as this.
In the Ultimate Spider-Man episode "Damage", Spider-Man accidentally hits Nova with a Shrink Ray used to aid in clean-up after super-hero battles (by reducing the debris to more manageable sizes); Nova is stuck at action figure size for the rest of the episode.
In Mulan, Mushu is a very tiny dragon. He says he's "travel sized", but he really is that small. He is still not a lizard.
Various breeds of animals are bred for size, presumably because of cuteness: dwarf cats, chihuahuas, poodles...
Japanese culture is obsessed with cuteness, and this is a part of it.
Shelties are adorable mini-sheepdogs that were bred for an adorable reason: to herd tiny sheep!
Miniature horses (often called ponies). Originally they were for hauling mine carts, now they are now being tried out as a substitute for guide dogs. (There are vastly less people allergic to horses than dogs, and horses have very long life spans.)
Pomerianians were bred specifically to be small after Queen Victoria both popularized the smaller types, and led a breeding program to decrease their size.
Miniature dachshunds. When they're nasty, they're really nasty... but when they're nice, they're sweethearts!
Poodles actually do come in normal-dog size (Standard Poodle) as well as yappy-dog size (Miniature Poodle and Toy Poodle). Standard poodles are actually quite intelligent, and can be aggressive. The infamous "poodle cut" that the smaller versions are known for is actually a perverted, decorative mutation of the more functional haircut they used to be given in their capacity as hunting dogs.
An unfortunate Deconstruction of miniature pets: many "teacup" breeds, especially dwarf cats, suffer from genetic and physiological diseases due to inbreeding and severe dwarfism.
In biology, this is termed neoteny (the appearance of being youthful) and is one reason men are often attracted to women who appear younger than them (ie. being shorter and having smaller features overall). The inverse is Amazon Chaser.
In the United States, small candybars mostly given during Halloween are marketed as "fun size."
The Aussie Racing Cars series, a series featuring silhouette race cars (eg. every car runs the same equipment, in this case a turbocharged 1.2L Yamaha motorbike engine mated to a sequential transmission) with body styles that resemble scaled down versions of famous cars that have participated in the V8 Supercars series at some point in history.
Narrow-gauge trains, especially the old steam engines that look like big toys. They are about the same height as a person, and their form of railroading feels much more personal than that of the big trains.