Bishi Bashi: The parodic minigame Arrow Basher! has characters performing various martial arts moves on a cliff, before transforming with Stuff Blowing Upin the background. Failure results in an Ash Face instead.
Cassette Beasts is a game in which people transform into mons in order to defend against them.
Dawn of the Monsters: Eiji Murasame was mutated by Sheol energy and gained the ability to transform from a human into an Ultraman Copy called Aegis Prime.
Sister Leica from Demonbane can transform into white angel Metatron, something unique to the visual novel and left out of the anime adaptation.
Digital Devil Saga has a very dark example. After contracting the so-called Atma virus, the human gets the ability to change into a super-powered Atma Avatar, able to use magic and various other abilities. However, the infected must consume flesh of other infectees, lest their mind will be permanently consumed by hunger. Most enemies in both games are actually Atma Avatars, who your party kills and eats. The book series clarifies that there are two types of Atma Avatars - Lesser, which are shared by multiple people and happen to look like demons from the greater Shin Megami Tensei series, and Higher, which are unique, more powerful, and happen to belong to major characters.
The player character in the NES title Dragon Fighter is a gladiator who can turn into a fire-breathing flying dragon once a transformation meter fills up.
EXTRAPOWER: Attack of Darkforce has Torajiro and Ryo who, with the power of the Guren Stone and the Gecko Stone, transform into GUREN TIGER and GECKO WOLF!
The main character in Illusion of Gaia has three forms (including his normal form), all of which have different powers.
In Kingdom Hearts: Birth by Sleep, Terra, Aqua, Ventus, Eraqus and Xehanort are all Keyblade wielders, and all have special Keyblade Armor that they can use whenever in combat or traveling through space. While it is unknown how Eraqus and Xehanort activate their armor, Terra, Aqua and Ventus transform by smacking the small amount of armor visible on their normal clothes (for Terra and Ventus in particular, it's their singular left shoulder-pads). The main trio can also toss their Keyblades up in the air to turn them into gliders to travel though space on.
In what is perhaps the coolest part of the game, since Keyblade Armor protects its wearer from the darkness, Terra activates his in a last ditch attempt to avoid possession by Xehanort (who is essentially a Dark Lord), and while his body is still possessed, his heart trapped within, his mind manages to escape and inhabits the armor, creating the Lingering Will (which originally appeared a secret boss in Kingdom Hearts IIFinal Mix), which you then play as against your possessed self, essentially making it Henshin vs. Henshin User.
Dragoons in The Legend of Dragoon can transform between their civilian and powered-up, armored forms, getting access to magic spells, flight, and greater strength and endurance in the process.
In The Legend of Zelda: Majora's Mask, four of the masks Link collects on his journey through Termina transform him into the being they depict: the pond-hopping, bubble-spitting Deku, the fast-rolling, fire-punching Goron, the fast-swimming, boomerang-launching Zora, and the mighty Fierce Deity.
In The Legend of Zelda: Twilight Princess, Link eventually gains the ability to change into his wolf form and back at will, which grants powers like increased senses.
The most straightforward examples are Geo and Sonia from Mega Man Star Force, who become Mega Man and Harp Note by undergoing a Fusion Dance with Energy Beings Omega-Xis and Lyra. In fact, most of the cast undergoes such Henshin, but heroes are in the definite minority. The process actually bears a certain resemblance to Cross Fusion from Mega Man NT Warrior, listed above.
In the Mega Man ZX series, a Mega Man is a person able to use a Biometal to transform in a process called "megamerging". Like Star Force, since some villains also have Biometals, the series also has "Henshin Villains".
Even the original Mega Man was prone to it, since he had a non-combat form he spent most of his time in; that said, the audience almost never gets to see Rock in his off-hours, so sightings of the change are few and far between. He does it in the fifthGame Boy game, though. No invocation, he just jumps into the air and transforms from Rock to Mega Man. It doesn't help. A short mini-comic also implies that his helmet can be used as his henshin device.
In numerous Metroid games, finishing with a good time or high percentage of items collected will typically show Samus removing her suit instantly, often in a flash of light. In Metroid: Zero Mission she removes her suit this way just before getting shot down, and then acquires a new suit that forms around her. As of Metroid: Other M, it is demonstrated that Samus' Power Suit is something that can only be sustained if her focus permits it, and will disappear if she loses focus, something which has been regarded as Fan Discontinuity.
Puyo Puyo 7 has a henshin game mechanic, where the characters turn into their older or younger selves.
Persona 5 has a variation: the Phantom Thieves don masks and unique clothing when they delve into the Metaverse, which is the only place where they can access their Personas.
Princess Peach becomes one in her second solo outing Princess Peach: Showtime!, being able to use "Sparkle" energy from the theater to take on transformations based on theater roles and using them to complete each play (level).
Red from SaGa Frontier is given the power to transform into the superhero Alkaiser by another such hero, Alkarl, in order to save his life.
Shadow Hearts series has so-called Harmonixers - people who can fuse with souls of otherworldly creatures, taking a monstrous form. The exact nature of their powers and abilities seems to vary from person to person, but they are inherited genetically.
Most Harmonixers can assume only one form, which seems to be the norm for them. One such Harmonixer, Kurando Inugami, however, was able to get a second form. There's also Jinpachiro, Yuri's father, who at one point turns into another form, Seraphic Radiance, but given the circumstances, it's unclear if it were his actual powers.
Yuri Hyuga, the protagonist of the original Shadow Hearts and Covenant, has the power to transform into a number of different forms, but he has to consume souls of monsters he kills to unlock them. Having so much souls inside him did a number on his psyche, and in the first game he suffer from a mental case of Painful Transformation every time he fuses.
Shania, the main Harmonixer of From the New World, has to contract spirits of nature to gain their powers. As a result, she has less fusions than Yuri, but her transformations are not painful, and result in Cute Monster Girls, rather than grotesque monstrosities.
Kouta Asuma from Super Robot Wars: Original Generation has ability to transform into Fighter Roar, he later join by his sister Shoko Azuma as Fighter Emmy.
Viewtiful Joe, with wonderful catchphrases to go with it: "Henshin a Go-Go, Baby!" and "Henshin Around!". It just so happens that he only actually needs to say "Henshin". The rest of the catchphrase is just for fun. When Silvia and Blue transform, they just say "Henshin!" without the rest. His Evil Counterpart mocks the phrase, which is the stinger to this page, but has his own Henshin phrase: "Devil Trigger!"
When you go to the 1950s in Yo-kai Watch 2, your grandfather Nathaniel/Kenny (depending on whether you play as Nate or Katie) is a Kid Hero obsessed with the television superhero Moximous Mask.
The titular hero of Cosmo Police Galivan begins each stage as an ordinary human in civilian garb, but dons cybernetic armor upon picking up a power-up item. The arcade flyer even depicts a Toku-style Transformation Sequence, though this is not seen in-game.
Ys IX: Monstrum Nox has titular Monstrums. Upon bein hit by a magic bullet person gets an ability to transform into superpowered alter-ego, which is basically just them, but with Impossibly Cool Clothes, outlandish hair color and a minor case of Red Right Hand. They also get a single superpower, like Super-Strength or Wall Run, called "Gift", that they can share with other Monstrums. While exploring city of Balduq, they constantly transform, using Monstrum forms for Roof Hopping and normal identities for talking with civilians.
No More Heroes III: The Badass Normal Travis Touchdown can enter a Kamen Rider-esque Full Armor mode if he scores triple-7s on the Slash Reel or during set sequences in the game, which gives him a massive boost in power for a short time. He'll even call out "Henshin!" when transforming sometimes.
even depicts a Toku-style Transformation Sequence, though this is not seen in-game.