After Superman comes back to life during Reign of the Supermen, he joins Steel and Superboy in assaulting Engine City, a gigantic engine built over the ruins of Coast City by Mongul and the Cyborg Superman.
During the JLA's "World War Three" story arc, Superman invades the eternal engine an intergalactic threat named Maggedon has sent to Earth.
The ancient underground Krell machinery, which was roughly 40 miles long on one side, in the sci-fi classic Forbidden Planet.
40 miles long, in the shape of a cube, and full of fusion reactors. The amount of energy output is enough to power all of a (long dead) civilization's needs, or blow the planet to smithereens if set to overload because humankind is not ready.
In the 1997 version of The Borrowers, a milk-bottling factory is this from the Borrowers' perspective.
V'Ger in Star Trek: The Motion Picture is a machine so vast it could (as Uhura and McCoy say "hold a crew of tens of thousands...Or a crew of 1,000 that are ten miles tall," and the 'Enterprise' spends a large portion of the film inside it. When viewing V-Ger's holographic memory, Spock sees a "machine planet' which he speculates may be V'Ger's homeworld.
Ember in City of Ember is not all engine, but between the generator and the pipeworks a lot of it is made up of constantly running machinery.
In Andre Norton's Uncharted Stars, the Forerunner factory world to which the star map bowl led, which was the source of the zero stones.
The Death Gate Cycle featured a floating island-machine, the Kicksey-Winsey. This machine is so vast and complex that in the centuries after its designers had abandoned it, the enslaved dwarves left to run it have turned their acts of maintenance and assembly into a religion; they no longer understand why the machine does anything, but have managed to keep it operational.
The young Jedi Knight series and some other Expanded Universe books include the rocky planet Mechis III. The entire planet is covered with droid factory complexes and during the reign of the Empire it was even owned by a single company, Arakyd Industries. Less than 100 biological employees live on the planet, the rest of the population is millions of droid workers. And yes, Mechis III has plenty of volcanic activity, so it has elements of Lethal Lava Land as well.
In Roger Zelazny's Jack of Shadows, there is a Machine at the Heart of the World (the purpose of which is to stop the Earth from rotating).
In Timothy Zahn's Spinneret humans stumble, by sheer chance, on a huge alien machine hidden inside a mountain, which has been dormant but active for millennia. It turns out to be a gigantic extruder, which absorbs any metal in and on the planet itself to make super-sticky string, originally destined to shield a whole solar system from detection. It houses enormous amounts of machinery, not to mention an artificial environment for the original workers and at least one fully working spaceship.
In Anne McCaffrey's The Ship Who Won, the "magic" discovered on an alien world is powered by an enormous weather-control system inside the planet, which the mages are abusing to cast "spells".
In Babylon 5, the Great Machine of Epsilon III was an homage to Forbidden Planet. It is seen in the episodes "A Voice in the Wilderness", "The Long, Twilight Struggle", "Voices of Authority" and "War Without End".
Homage in the sense of a 1990's remake complete with giant vertical shaft with elevator globes.
The Doctor Who 16th season story The Pirate Planet, which was also Douglas Adams' debut as a writer for the series, features a planet that exploitatively harvests raw materials. The Doctor must undertake some very risky maneuvers in order to shut it down.
On a much smaller scale, the Planescape campaign also has The Foundry, a huge factory in the Lower Ward of Sigil that was the headquarters of the Godsmen. Unlike most examples of this Trope, it had a known and useful purpose (it made all metal goods needed in the city except weapons, such tools, nails, pots, pans, and utensils) but it could still be used in any adventure that called for an Eternal Engine.
There's also the lower levels of the Imperial Manse, a superweapon capable of annihilating small countries with a shot. It was built by Autochthon (the aforementioned god, although he's technically a Primordial, which is a step up), who can't be harmed by machines, so he didn't really think to put up much in the way of safety around the giant gears, pistons, plasma jets etc.
On the other hand: do you really want someone who ISN'T exceptionally careful, logical and prudent to get to the controls of the most powerful weapon currently in creation?
Many of the Imperium's typical "manufactora" in Warhammer 40,000. Calling one a "small city" is a severe understatement for some of the bigger ones. Then you have the Forge Worlds, which are entire planets covered with factories and industrial facilities.
Necron tomb complexes often carry this theme, though Necron technology bears little resemblance to human tech, or anybody else's for that matter. Case in point being the World Engine.
One of the most overboard was from the same game as the Trope Namer: Cannon's Core, the Magitek innards of a space station built using modern robotics and ancient mysticism. The deeper the characters went, the more the mystic elements began to eclipse the mechanical ones.
Asteroid Coaster is a straighter example from the same game. Mixed with Big Boo's Haunt and Theme Park of course, but it's where Eggman converts the wisps to the Negawisps. Sweet Mountain has very slight elements of this.
The aforementioned Chemical Plant and Planet Wisp both reappear in Sonic Generations.
Sonic CDcombines most levels' current setting trope with this in bad futures. Wacky Workbench is this in the Present and Past as well as the Bad Future, but becomes Toy Time in the Good Future. Metallic Madness is this full-time.
There's also Final Fantasy VI's Magitek Research Facility in Vector. Conveyer belts, a trash dump, and big glass tubes of chemicals with Espers inside, being drained of their magical energy courtesy of not-so-mad scientist Cid. All set to the track 'Devil's Lab', which can only be described as industrial rock with piston percussion, growling electric bass and organ, and strings.
Even as far back as Final Fantasy IV, we have a rather interesting case, namely when the party enters the Giant of Babil.
Commander Keen: The second installment is set entirely within the Vorticon Mothership, while the fifth installment is set entirely within the titular Armageddon Machine. Both settings feature most of the classic hazards, as well as evil machines (cannons in the second game, generators in the fifth) that have to be disabled so the titular character succeeds on his mission.
Grunty Industries, Nutty Acres and Logbox 360 from the Banjo-Kazooie series.
BioShock features Hephaestus, described by the soundtrack as "the Engine City." It's an enormous power plant that funnels geothermal energy (and what looks like magma) through colossal engines to power all of the underwater city of Rapture. However, it's not especially "eternal," as, like all the rest of Rapture, it's in the process of falling apart, and one of the missions involves strapping an EMP bomb onto one of the engines.
The third quarter of the original Crash Bandicoot (1996) consists mostly of this (levels such as Heavy Machinery, Cortex Power and Generator Room), with Crash roaming through Cortex's enormous power plant which, on the surface, doesn't seem to serve much of a purpose other than to dump tons and tons of radioactive sludge into the nearby oceans.
The Gremlin Village and the It's a Small World ride in Disney Epic Mickey are filled with gears, steam-leaking pipes, and generic steampunk elements. Both cases are justified, since the Gremlins are all mechanics and most, if not all of the rides in the Cartoon Wasteland probably use outdated technology. (Except for Tomorrowland, of course.)
Defender of the Future has about a quarter of the game be one of these due to the Man's Nightmare levels, which has you following the process of mining rocks for crystals to the end result down the factory line, over the span of multiple, multiple levels. Not half as annoying as it sounds because the place is designed so well.
The Dwemer ruins in The Elder Scrolls III: Morrowind are powered by geothermal energy and manned by complicated enchanted automations who mindlessly perform security and minor repairs on these forgotten cities. The Dwemer were also about to experiment with the power of a dead God when they were cast out of reality by it.
The Residue Processing stage in Half-Life certainly qualifies here.
In Mario Kart, Toad's Factory, a race course from Mario Kart Wii, features some elements of this trope, being a factory with crushing machines, conveyor belts, a steam room, and bulldozers that move back and forth periodically across a mud path at the end of the course.
...and Spark Man's level from Mega Man 3, and Dust Man's level from 4, and Mercury's level from V for the Game Boy, and Junk Man's level from 7, and Grenade Man's level from Mega Man 8, and Plug Man's level from 9...it'd probably be easier to list the games that don't have one. As with the Sonic series, justified by Wily's Mad Scientist nature.
Mega Man X has Flame Mammoth's factory. With inconveniently placed conveyor belts that crush rubbish for no particular reason. Megaman X 6 also had Metal Shark's stage as one of these.
And in ZX, the entire world itself is basically cybernetic to an extent.
Happens frequently in the Metroid Prime series, to varying degrees. Magmoor Caverns in the first falls into the "combined with Lethal Lava Land" variety, and the Phazon Mines have their fair share of machinery obstacles. Prime 2 features the technologically-themed Sanctuary Fortress, and Prime 3 has the Steampunk-inspired region Sky Town on the planet Elysia, complete with enemies with names like "Tinbots", "Steambots", and "Steam Lords", and the Pirate Homeworld.
Metroid Prime Hunters has Samus morph ball into a boiler and dodge its eternal workings while trying to find something.
In a bit of Fridge Logic, Sekto keeps two large reactor type objects that he apparently uses as weapons right next to his desk, which like most equipment in an Eternal Engine, will explode if you shoot it enough. Apparently he either really wants to be a Load-Bearing Boss, or he doesn't care about his own safety.
Not to mention the entirety of Rupture Farms, which half of the first game takes place in.
The behind-the-scenes sections of Portal's Aperture Science Enrichment Center, excepting the (scarce by comparison) office areas.
The sequel takes this up to eleven, where apparently the entire facility's operations is to churn out products for testing against other products. While there are facilities to manufacture products (indeed Wheatley apparently was able to design and mass produce his own robots) there seems to be no way of shipping them, only to continue sending them back into tests. GLaDOS and Wheatley also seem to have little else other than to continue testing for their entire lives.
Most of Prey takes place in a planet-sized Eternal Engine. The aliens live in a giant artificial sphere in which every room, corridor and passage is strewn with wires, pipes and machinery of all sorts (not always inoffensive).
The factory level in Quake II was a large complex in which human and mechanical parts were cut'n'pasted together (with no anesthetic...) to form Strogg soldiers. The machinery had more psychological effects and less gameplay consequences than most Eternal Engine environments, but the player was required to avoid a giant crusher or two and step on a few conveyor belts. Activating the human-mulching machines was optional.
The image at the top is of the Steel Works level from Sparkster for the SNES, although it's far from the only Eternal Engine level in that series; at least half of the levels in that series could be considered variations on the concept.
The same game also features the interdimensional spaceship(s) of Tempest Keep (including the Exodar, which serves as the Draenei races' home area), although the hazards normally inherent to Eternal Engines do not show up here, limiting the use of the design to be mostly thematic in purpose.
Various bits and bobs of Titan technology can be found throughout Northrend. Many of them seem to be gigantic engines of some kind, though very few of them are working.
The ruins of Uldum are less about gears and more about beam emitters, computers and robots made out of stone.
The FireCage in An Untitled Story is an abandoned but still partly operational underground factory or power plant of some kind. The pools of molten metal or rock found here and there give it elements of Lethal Lava Land.
Jazz Jack Rabbit: The planets Tubelectric, Letni, Orbitus, Technoir, Dreempipes, Industrius, Deckstar, and the Megairbase and the Twin Battleships. Also the abandoned lab levels in Jazz Jackrabbit 2.
Shadow Complex has an area like this. Justified in that the purpose of the factory is explicitly explained as building the mechs and weapons.
Dungeon Siege and its expansion Legends of Aranna both feature these, both populated by Goblins, themselves mechanical creatures. The former is the goblin's home, and the latter is the great clock you've been heading for the entire game.
There are a couple massive ones in Blue Dragon, and at the end of the game you find out the entire planet is one. The term "Eternal Engine" itself is used to refer to the Ancient machine's power sources.
Klonoa 2: Lunatea's Veil features the factory levels in Volk, constantly churning out bombs, planes, and, apparently, soldiers for Volk's neverending civil war. The Maze of Memories level may qualify as well, though the 'machinery' all runs in the background, and doesn't seem to affect gameplay at all.
Pokémon has its various power plants. It's not as severe as some examples, since the other danger in them is the hordes of Electric and Steel monsters and the occasional lightning bird.
Terminal Velocity has the Moon Dagger in episode 1 (essentially a huge spaceship), and the massive supercomputer planet which makes up the last two levels of episode 3.
The entirety of the Arca Plant levels in Phantasy Star Zero. Mechanical enemies, machinery in the background that becomes larger and more complex, and a giant robot at the end who more than counts as a That One Boss to a degree that the final boss and bonus boss seem like child's play in comparison.
Although mentioned below for its other appearances in fiction, the planet Cybertron in Transformers: War for Cybertron is worth noting, since it is literally an entire game set inside, outside, and on top of a massive eternal engine. It even features a level inside another character who is himself an eternal engine.
The Primagen's Lightship and the Oblivion Warp Portals from Turok 2 would both count. However, the Portals are more true to the aesthetics of the trope, as each one contains a healthy dose of grim, industrial architecture complete with pumping pistons, steam valves, chains dangling ominously from the ceiling, pits of magma and all the other goodies.
The Sun Temple in Aquaria is a clockwork Eternal Engine; you can even pilfer the key and use it to decorate your cave (which inexplicably has chambers constructed in the style of every locale you visit, including the Sun Temple). In spite of having supposedly been abandoned for quite some time, it's still running and shows no signs of decay; possibly the clockwork sea life lurking around are automated maintenance staff, keeping one another wound as well as making sure the temple stays in working order, after their masters are long dead.
Legend Of Kalevala has an underground factory area underneath the first area. It's full of Floating Platforms, and it's the first place where you'll find Lava Pits. This area is one of the tip-offs to the protagonist that the former inhabitants of Kalevala were a very intelligent civilization.
The Baten Kaitos games have the city of Mintaka, which is built out of pipes that are constantly emitting steam of some sort. Origins refers to it as 'machina' and discusses the ethics it presents.
Origins also has Tarazed, which is a man-made airship the size of a continent.
Resonance of Fate has Basel, which is not only an Eternal Engine (of gears!), but is also the entire Overworld Not to Scale in which where the game takes place, and is apparently the last bastion of human civilization. Not so eternally however, it's at its last legs by the game's start.
The planet "Facility", in the BattleZone II mod, Forgotten Enemies. The planet is covered almost entirely in machinery, with huge cranes, fuel tanks, and heat sinks dotting the surface. The atmosphere is tainted green, and the only exposed land is brown, lifeless rock.
World 6-F1 (RGB Factory) in Super Mario Fusion Revival: This fortress level takes place in a high-tech factory with three distinct areas: a red area (lava and fire), a green area (overrun with plant life), and a blue area (a swimming area). This is a key hunt level with a central hub that leads to a boss fight with Dobkeratops of R-Type fame.
From Sly Cooper And The The Thievius Raccoonus, a couple of levels in Sir Raleigh's fortress take place in the engine rooms, complete with enormous cogs and gears, fiery furnaces, and electrically charged fan-blades.
Tiny Toon Adventures: Buster's Hidden Treasure has a factory as its final world, complete with various robot enemies, spikes, electric reactors, a lava-filled floor in the third act, and various spinning gears, wrecking balls, and platforms Buster must maneuver across to get past them.
The Taz-Mania video game for the Sega Genesis/Mega Drive has a robot factory as its second world. Various hazards include spinning blades, furnaces, hammers, laser cannons, tunnels that shock you which you have to find the right switch to temporarily turn them off with, and decoy switches that shock you when you pull them.
Team Meat's Meat Boy features the Salt Factory, which features buzz saw launcher, salt and even rocket launcher.
Stage 7 of The Legendary Axe II is this, even though it's supposed to be someone's royal palace.
Many areas in Spiral Knights, particularly the Ironclaw Munitions Factory. Given the constructed nature and the ever-shifting mechanized innards of Cradle, the whole planet is arguably an Eternal Engine.
Batman: Arkham City has the Steel Mill. A very realistic example, too. The only Lethal Lava Land type area is the furnace you go through when you start off. Everything else, well, the mill is just the base where Joker is hiding out and isn't running, making this a Subverted Trope. Batman has to make things run himself to get through it, hitting switches and getting (more like making) a gadget that lets him fire Remote Electric Charges to power devices. The conveyer belts are completely still, even, except for one secret area where you complete a batarang mini-game for a trophy.
Chrono Trigger has you go through one on your first trip through The Future. Although it's a factory, you're required to go through it to power a machine in a different location. You can ride conveyer belts, operate cranes and fight rogue construction bots.
There's also one much later in the game, although it isn't an actual factory. It's called Geno Dome, or in the japanese version, Genocide Dome. Halfway through the level, you find out exactly what the factory is running for: Humans systematically being murdered so that only robots are left to rule the world.
The radioactive waste plant in Teen Titans is a very good example.
Slade had one for a lair during the first season. And guess where he chose to reveal himself to the Titans after coming back from the dead?
The planet Cybertron in Transformers. In its various incarnations it is depicted with all kinds of huge machinery all over the planet, with good reason - the entire planet was a Transformer. Then there is Unicron, whose insides are an even more literal take on the Eternal Engine Planet trope, and his tentacle horror Japanese cousin Dark Nova. The later US comics from Marvel also introduced the Decepticon War World.