In her defense, in potential justification, she's a traditional oni, allegedly responsible for performing impossible feats of strength and mysticism in Japanese lore. Further supplemental material has her boast that she is a better magician than her fellow oni Hoshiguma Yuugi, who is outright stronger.
The spirit channelers of the Ace Attorney series change their body shape and size to what the channeled spirit looked like when they were alive. Many mechanics of channeling, including the question where the extra mass comes from (or goes to) go unexplained in the series. Channeling is tantamount to magic, mind you.
Numerous cases in the Resident Evil series, where injecting oneself with any of the mutating serums tends to cause the subject to double in size and sprout all manner of tentacles and spikes. In Resident Evil 5, Irving goes from being about 5ft tall to twice the size of a blue whale in about 10 seconds. They truly outdid themselves with Derek Simmons in Resident Evil 6. Not only does he grow into a massive T-Rex thing about the size of the average office building, but he freely transforms back and forth between this and his human form during the fight with absolutely no explanation of how it's possible. Even worse, one of his attacks is to shoot his own bones as ammo like an organic gatling gun. Good luck figuring that one out.
Metroid Prime 3: Corruption: When fighting Gandrayda in Pirate Homeworld, she transforms into multiple characters you've already fought over the course of the game. Most of what she transforms into is sensibly around her own size, with the notable exceptions of a group of tiny Swarmbots (while they may collectively equal her size, she turns into multiple beings at once), Ghor and his ginormous powered-armor, and the massive Berserker Lord. Her scan page states that how she can change size so drastically is unknown.
Metroid Fusion: X-Parasites tend to do this while mimicking creatures. Most creatures of roughly human to twice human size will require just one X, despite the X only being about the size of a basketball. Some other creatures, like certain Space Pirates, will require two or more (Golden Pirates have five for some reason) and bosses will generally have a larger Core-X surrounded by smaller X, showing at least a semblance of realism.
Where exactly does Samus stuff her body when she goes Morph Ball? This is at least lampshaded in Metroid Prime, where one of the scans in the Phazon Mines reveals that the pirates attempted to copy morph ball technology, but... well, the results weren't pretty. If you peek in between the two halves of the Morph Ball in the Prime series it appears to be a case of Samus being converted into Pure Energy.
[PROTOTYPE] averts this rather well. Size-wise all the people Mercer absorbs are about the same size as him. It's also strongly implied (though never stated) that Mercer weighs significantly more than a normal person does. Falling more than a few feet causes the pavement to buckle underneath him when he lands - falling great distances sends out a massive shockwave that can throw cars aside and kill bystanders, which gives him plenty of mass for his larger powers (such as his Whipfist or Shield) or denser powers (Hammerfists, as in the page quote, and Armor).
Also, whenever Alex uses his non-shapeshifting powers (like super-strength or clinging to walls), there's an effect that seems to imply mass is being expended. We see a similar effect when he's gliding. This seems to imply that he's "burning" the extra mass, keeping himself from getting too heavy.
Try standing on a vehicle - most cars and other vehicles will be unable to move, and even tanks are slowed down by his weight. Using thermal vision, Alex is also far, far warmer than other humanoid entities (such as civilians, soldiers, etc.). Whether this is to make him easier to see and control for the player or yet more suggestion that he has much more mass is unknown. In thermal vision, Infected also appear brighter than normal civilians and even soldiers, which could imply that, like Alex, they are far denser than ordinary people.
One has to wonder that if Alex has all that mass to create craters from very high falls and elbow drop with a heavy hammerfist to shatter armor among other things, how is it that he can flip (by tapping the jump button) onto a normal car (from the same level) and walk onto its roof and not have it crushed under what is supposed to be exceedingly heavy weight over a small area (a pair of feet)? After all, to throw an army truck without shoving himself in the opposite direction, he needs to possess a comparable amount of inertia himself, hence a cab-crushing amount of mass.
Unless of course he uses biomass to "adhesively" secure himself to the ground before throwing stuff that should still weigh a lot more than him. Doesn't really explain air-throws though.
As long as he takes off his shield and armor, he can sprint as fast as a car and still trivially knock people down non-lethally... anyone?
Perhaps his armored shell prevents him from properly flexing and articulating his limbs as quickly as he can normally.
Even better: Ever tried shoving someone right next to a deformable object/terrain? What should been a shove that pushes someone moderately, if you miss, can dent cargo containers, vehicles, even a military base exterior fortification wall!
Project Eden has rats that transform into monsters over twenty times their original size, then turn into a small splash of green goo when they die.
The Tank◊ in Left 4 Dead. According to the game, it takes place just a few weeks after the first infection. Yet, you regularly meet up with the thing pictured above.
The same could be said for The Charger in Left 4 Dead 2, where his arm has become massive and covered with callouses.
The Smoker, and to a lesser extent the Spitter, has somehow become much taller than an average human. The Smoker's tongue would also appear to be an example at first glance, but if you look closely enough you can see that they still have a normal tongue in their mouths and they're actually shooting something else out to grab survivors with (typically theorized to be intestine).
The Boomer is an aversion, as their girth is all gas; their bodies have become swollen with noxious gas and bile that fills up in large boils across their body, which also means they only take about as much punishment as the regular, non-mutated infected before that gas causes them to pop like a balloon.
In Halo 3, the Flood has a pure form (which aren't based on an individual infected being) which can change its shape for various functions. Interestingly, the mobile form is quite small and light, but it can change into a large "tank" form in a few seconds which is significantly more massive, and its shooter form should be losing mass as it shoots, but it has no effect on its ability to change again.
Averted in Mega Man X with Axl; he has a copy chip that allows him to transform into any Reploid he has a genetic sample from, as long as said reploid is approximately the same size as him. However it's played straight with all the other new generation reploids (from which Axl is a prototype), some of which can shapeshift into the 8 bosses, and Sigma, all of whom are of different sizes. In Mega Man X4 it's safe to assume Double keeps the extra mass in his huge gut needed to transform into his twice-as-tall combat form complete with Wolverine claws.
Clayface in Arkham City is a gargantuan monstrosity, towering well above anybody in the game including TITAN henchmen and Bane. And yet in the whole game he takes the form of the Joker, possibly the thinnest character in the game. He could theoretically be completely hollow inside, but then his hammer-hands attacks would probably not hurt that much. Maybe he left most of his mass in the theater, while only going with a smaller body's worth to the steel mill. That's why the theater is boarded up - Clayface is still in there. Its also possible that he is extremely dense and used his acting and shape shifting abilities during the fight with Clayface!Joker just before Protocol 10 to fool Batman.
Averted in a plot-significant manner in Flashback: The game revolves around shapeshifting aliens infiltrating humanity. The tell? They're extremely dense as a side effect of having enough mass to shift to larger forms — the protagonist first discovers them with the aid of glasses that can analyze molecular structure and determine an object's density at a distance... and suddenly discovers people that have a far higher density than seems to make sense.
The Thing (2002): Whitley goes from an ordinary Man-Thing to a ten story high monster when he finally transforms for the Final Boss fight.
In NetHack regeneration is handled realistically - while under any sort of rapid regeneration effect (either granted magically or naturally), your hunger meter will drain 50% faster than normal. Polymorphing however, is not - you can polymorph into anything from a tiny bat to a gigantic dragon with no explanation for where the extra mass comes from or goes. Some monsters will do this regularly, such as wererats which rapidly shift between human and rat forms, or chameleons, whose natural form is the same size as a real life chameleon but who can change into any other creature in the game.
World of Warcraft's druids can shapeshift into a cat, a deer, a bear, a bird, a seal, an owlbear, and a treant. No mention is ever made of how this is actually possible. It's not that they make their mass less dense, since the bird can actually fly and the deer can carry a rider. How it is physically possible for a 9 foot Tauren to become a cat boggles the mind... much less how a warmblooded mammal becomes a treant. Especially since shapeshifting doesn't even cost mana. The game's magic usually makes some degree of sense, even if it violates the real world's laws of physics (often it-at least canonically-obeys the law of conservation of energy, for example). This though, makes no sense at all.
There is also the polymorph spell, which can temporarily turn anyone into a sheep (or pig, or frog). Player characters range in size between 4ft and 9ft, and polymorph can also be used on a warlock's demon pets (who can but up to 12ft in height). Again, no explanation is offered for how this works.
There are also the dragons, who can take the forms of humanoids as they wish. Dragons are enormous creatures, but they start out tiny. Tiny whelps can take the shape of a human child, and collossal adults can take the form of a human. There's a 2ft difference between a human child and a human adult, while there's a 6ft difference between a whelp and an adult. How this works is anybody's guess. It's not an illusion, since a dragon who encounters itself via time travel shenanigans can't shapeshift.
Prey (2017): Typhon Mimics, despite being no larger than a dog, can perfectly imitate anything from a pen to a shipping crate. You can find an email chain in-game from a group of scientists trying to figure out how it works, with theories including a 'fake' shapeshift using directed hallucinations, swapping places with the desired object in an alternate dimension, and, in frustration after many inconsistencies are pointed out with the others, 'magic'.