For mostly peaceful versions, there are the Koru behemoths, largely invincible creatures that wander a set migration track and have ecosystems and cultures dwelling on their backs. Some of them have quirks such as killing any dragon that comes too close or taking a dip in the Iron Sea for the fun of crushing a bunch of sea monsters.
For less peaceful versions, there are the greater fomori, which are world-destroying horrors as large as Koru behemoths and which can warp reality to create horrors in a grand scale. If they returned to the world, even if for such a brief time as an hour, they could destroy civilisation and usher the world into a 14th Age.
Underkrakens are gigantic eldritch horrors that lurk in the depths of the Underworld that might be cities or spaceships or monsters or gods, or possibly all of those things and more. The Underkrakens once unstoppably rampaged through the deeps, but for mysterious reasons are now mostly dormant. However, the soul flensers (their inhabitants, crew, servitors or emanations) have gone forth to steal soul fragments to reawaken them.
Gulmagul All-Eat-All is a gigantic demon the size of a flying realm. Characters can hop onto his back and move across him — he's a landmass as well as a monster. His ultimate desire is to eat a Koru behemoth and become the largest predator in existence. He will break the world by eating it.
ChampionsHero System Bestiary. The Hach-U-Rui are giant Japanese reptiles (minimum of 100 meters tall) that can survive hits by howitzers and may have an energy breath weapon. In short, they're the Champions equivalent of Godzilla.
The Creature That Ate Sheboygan, a wargame from SPI, is about the title city being attacked by a giant monster. One player defends the city with the National Guard and the other plays the monster.
The signature feature of The Day after Ragnarok setting is the corpse of one of the largest kaiju ever seen — Jörmundgandr itself, summoned up by Nazi mystics in the final days of an already-alternate history WW2 and killed only by a brave American aircraft crew making a hasty suicide run to deliver a prototype atomic bomb straight into its eye. The body of the Serpent covers large stretches of Europe and Africa where it came down, and there are hints that it was growing rapidly between its initial manifestation and its death and hadn't even reached its full size yet.
"Kaiju" is a template (see Dragon #289), enabling the DM to turn any Animal, Magical Beast or Vermin in the Monster Manual into a fifty-foot armour-plated monstrosity capable of destroying TokyoNakamaru.
Older Than They Think, as the old Basic/Expert/etc version of the rules had a proto-template for super-sizing normal monsters over a decade before that issue came out. They also had critters that qualified as this trope right out of the box, like the earthquake beetle.
The original Oriental Adventures supplement introduced a number of creatures called "gargantuas" that were Captain Ersatzes of Godzilla, King Kong, and Mothra.
An adventure for the Oriental Adventures campaign setting, Test of the Samurai, featured a gigantic psychic monster called a "Krakentua", which is best described as Cthulhu, sans wings, in a kimono.
No discussion of giant monsters in D&D is complete without mentioning the legendary tarrasque. Only one exists on any given world; this reptilian monstrosity awakens every century to destroy everything in its path, devouring all life and reducing the countryside to rubble, and is completely unkillable without resorting to godlike magic. In later editions, if you DO manage to kill it, the Princes of Elemental Evil will just create a new one.
The Spelljammer setting has witchlight marauders, which function as both this and Eldritch Abominations. Their primaries are 200' to 500' long (secondaries are still massive, but much smaller, derivatives of the primaries at 20', and tertiaries are human sized at 4' to 6' and still deadly), which were created with the explicit purpose of stripping life-bearing planets down to the bedrock. For true cosmic horror, there are the space marauders at over 1000' long, which create primaries and drop them onto planets and function as living spacecraft as well.
Spelljammer also featured a world crawling with tarrasques... with the twist that on that world, and only on that world (it was probably something to do with the atmosphere — the implication was that this was the homeworld of the tarrasque) they dropped the periodic omnicidal rampages for being docile lithovores.
True dragons are distinguished from lesser dragons (like wyverns) by their ability to never really stop growing, though diminishing returns tend to set in after about 1200 years. The oldest dragons, known as great wyrms, can easily dwarf a tarrasque.
On the topic of dragons and Spelljammer, stellar dragons are truly immense serpentine creatures who dwell in the phlogiston between the crystal spheres. The oldest stellar dragons can be three million feet long from tip to tail. That's 568 miles, roughly the length of the Italian peninsula!
Exalted has its share of giant, rampaging monsters.
Most of these are behemoths, created either by The Fair Folk for use in their reality shaping battles, or by the Primordials, for shits and giggles. Occasionally, an elemental dragon will ascend to such a level of spiritual development that it goes insane. Also, elder Lunar Exalted can use their Voluntary Shapeshifting to change into an incredibly strong monster that dwarfs cities.
One of the more distinctive behemoths of the setting is Juggernaut, Mask of Winters' undead citadel-beast that aided him in sieging Thorns.
And then you've got the hekatonkhires, which are often what happen when behemoths die. One of them, Vodak, ate a city.
In the Freedom City setting for Mutants & Masterminds, the Captain Ersatz of Marvel's Monster Island or DC's Dinosaur Island is actually called Kaiju Island. Its most famous inhabitant is Gigantosaur, who looks pretty much like Godzilla apart from being purple.
The game Gammarauders featured gigantic cyborg animals and dinosaurs with a variety of weapons sprouting from their bodies. Few things are more terrifying than a giant cybernetic Penguin waddling toward you, wrecking buildings as it comes.
King of Tokyo (with expies such as The King and Giga Zaur), and the follow-up King of New York.
The plane of Ikoria from Magic: The Gathering has giant murder-beasts, ranging from legendary beings of great power (such as Brokkos and Illura) to simple very large and hungry dinosaurs (Titanoth Rex). As part of a cross-promotion with Toho, some cards are even available as Godzilla promos, with Titanoth Rex being one of three cards used to represent the Big G himself (the others being Yidaro, Wandering Monster, and Zilortha, Strength Incarnate, which is only available as Godzilla).
The collectible miniatures game Monsterpocalypse is all about giant monsters (along with Humongous Mecha and alien invaders) duking it out.
In Numenera's Ninth World Bestiary there's the Titanothaurs. The Titanothaurs are monster rank 10 - the highest power level in the game. Between 3 bestiaries and the monsters included in the main rule book, there's less than seven Rank 10 monsters. Titanothaurs vary in nature, but the common thing they share is their massive size. Most are over 100 metres tall and all of them can regenerate even while in combat. Individually the Titanothaurs have unique powers such as Gravithaur generating a gravity wave or Suneko shooting plasma out of its eyes.
Obsidian: Age of Judgement from the defunct Apophis Corporation has a unique daemon type from the Carnivoria Domain and its master, the mindless and animalistic titan Abaddon. This unique daemon type is the Roamer and it's any mountain-sized Carnivoria daemon that's so large it's immune to any One-Hit Kill attacks. Destroying one of these usually takes lots of rounds of thermonuclear micro-nuke explosives.
The game introduces Kaiju as a monster type in Bestiary 4, defined as unique creatures of colossal size that hide away in remote places and come out to rampage when awoken - and yes, they fight each other. A number have been statted up by the gaming, including Agyra, a two-headed pterosaur with lightning powers and fair dash or Rodan in her inspiration; Bezravnis, a fiery three-tailed scorpion; Agmazar, an undead alien bioweapon; Yarthoon, a caterpillar-like being from the Moon; Vorgozen, a living mass of magical pollution; Lord Varklops, a King Gidorah Expy; and King Mogaru, a Not Zilla . They also have grand-sounding titles like the Forever Storm, the Inferno Below, the Star Titan, the Moon Grub, the Shapeless Feeder, the Thrice-Headed Fiend, or the Final King. In the default setting, most of them live in Tian Xia, specifically the Valashmai Jungle.
The Tarrasque, while still unique, is one of a whole family of unique kaiju created by the apocalypse god Rovagug. Which is itself an unbelievably gigantic insect-Eldritch Abominationimprisoned in the molten heart of the world in a cage whose bars are strong enough to hold it in, but wide enough to allow its comparatively tiny and ineffectual spawn to escape.
Beyond the Tarrasque and its siblings, we've got the Oliphaunt of Jandelay, Achaekek the Mantis God, and several non-unique monsters like behemoths (gigantic monsters sent by gods to punish mortal nations), and Black Scorpions and Deadly Mantises, based on the B-Movie horrors of the same name.
Pachimon is a Collectible Card Game from the 1970s, based on various toku media popular at the time depicting scores and scores of different kaiju (made by stitching together existing characters from numerous sources) destroying Tokyo (and later the rest of the world in their "World Tour" line).
The bestiary sourcebook of RuneQuest has a monster category called "Terrors". Terrors, such as the Crimson Bat of the Red Goddess, are unique monsters whose purpose is to show that there some things on Glorantha that are too powerful for any character to handle. Most of the terrors are truly massive, but even the smallest of them are much bigger than any human. Additionally even the most normal of the terrors is a bit off in their unnatural state while the strangest of them are a true Eldritch Abomination.
Star Fleet Battles includes a number of space monsters of various types (some living, some not), mostly for solo scenarios. One such scenario pays homage to the above game with the subtitle "The Creature that ate Sheboygan III".
Warhammer has some monsters that qualify, especially when you consider the Storm of Magic supplement. Not only are there straight up giants, but there are also Greater Daemons dedicated to each of the Chaos Gods. There is also the Chaos War Mammoth. Oh. and lest we forget the giant skeletons that the Tomb Kings use. The Dark Elves have an entire city dedicated to taming monsters, and among them are some very kaiju-sized creatures. Plus, there are even more of these creatures in the flavor text. In particular, the oceans are said to be filled with massive sea monsters.
The largest Tyranid organisms, such as the Heirophant, Dominatrix, Hydraphant, and Viciator, are classified as "bio-titans" as they are dozens of meters tall and wide and pack firepower and melee weapons comparable in strength and destructive power to their mechanical equivalents in other armies.
Chaos occasionally throws this trope into play. While it mostly only brushes this trope in the form of Daemon Princes and Greater Daemons, it sometimes comes out with a really big Daemon Prince or Greater Daemon. They do have the occasional variance, one of them being a giant Chaos spawn named Jibberjaw. While they do have kaiju, Chaos most often plays on the opposite spectrum of this family of tropes, as they sport super-heavy vehicles, most notably traitor titans, and the occasional super-heavy daemon engine, many of which arguably fit both tropes.
Yu-Gi-Oh! has an entire series of cards based on Kaiju, whose schtick revolves around summoning one to each side and having them fight it out. It even has a Field Spell based on the Tokyo Tower. Notably, to summon these, the player gets to tribute the opponent's monsters to get a Kaiju onto the opponent's side. As such, given that tributing is one of the few things that can't be protected against (most of the time), players favor using a Kaiju to tribute their opponent's hard-to-get-rid-of monsters and then wipe out the Kaiju before the opponent can even use it.
based on Kaiju, whose schtick revolves around summoning one to each side and having them fight it out. It even has a Field Spell based on the Tokyo Tower