Age of Mythology has the Lighthouse that can be constructed by the Egyptian, granting them an immense amount of line-of-sight that ensures that the Egyptian aren't caught off guard by an invading army. The Lighthouse is based on the Lighthouse of Alexandria, one of the Seven Wonders of the Ancient World.
The climax of Anchorhead takes place at a lighthouse.
In Animal Crossing, your town includes a lighthouse on the shore, and you may be tasked by Mayor Tortimer with turning the lighthouse on and off for a few days while he's out of town. In Animal Crossing: New Leaf, a lighthouse is one of the decorative structures you can build in your town.
Banjo-Kazooie has one in Treasure Trove Cove. There's a Witch Switch behind the lighthouse, and activating it fires a cannon in Grunty's Lair that uncovers a Jiggy. Banjo and Kazooie can also go inside the lighthouse, where they find a Mumbo Token, five musical notes, and another Jiggy at the top.
Beyond Good & Evil, in a subversion, has a nice friendly lighthouse where The Hero Jade looks after orphans until it is blown to bits.
BioShock: A lighthouse in the middle of the Atlantic contains a bathysphere station that leads to the destroyed utopia.
BioShock Infinite continues the tradition by having a lighthouse on the coast of Maine be a secret launchpad for a rocket ship that takes pilgrims to Columbia, the city in the sky. The game also depicts all the myriad worlds of the multiverse as lighthouses, shining like stars across the sky between universes, which is one reason the exterior of Infinite's lighthouse is identical to the one encountered at the start of the original game.
There's always a lighthouse, there's always a man, there's always a city.
In Breath of Fire III, the heroes have to relight a lighthouse that was shut down by faeries.
An annoying enemy structure in the tower defense Cursed Treasure 2. It provides a speed buff for up to 3 enemies in a huge range. Seizing this structure makes it shoot damaging fire beams on the enemies instead, making life easier.
The Barr Harbor Lighthouse is the last location the player is invited to investigate in Conrad Stevenson's Paranormal P.I.. The lighthouse itself and the surrounding grounds, which include the keepers' house, a barn and a cliffside cave, have a long history of paranormal interest, fueled by several stories and rumors of ghost activity. As a result the location has been a tourist attraction since long before it was officially turned into a museum.
The Curse of Monkey Island has Guybrush Threepwood repair a dilapidated lighthouse on Blood Island to summon The Lost Welshman.
Dark Fall 2: Lights Out takes place almost entirely in a haunted lighthouse. In several different time periods. Jonathan Boakes, the creator, based it on the Ballad of Flannan Isle.
A much smaller lighthouse is one of the prominent landmarks of Saxton in Boakes's The Lost Crown.
Dead Island features a lighthouse as a refuge at the beginning of the game.
In Dear Esther you start at an abandoned lighthouse.
The final location of the first Deep Sleep game, in which the only thing that can kill one of the Shadow People is the light from its bulb.
Diddy Kong Racing has one of the best uses of this. There's a lighthouse on the beach of Timber's Island that doesn't appear to do anything, until you beat Wizpig and win all 4 Grand Prix Trophies. The lighthouse then turns into a rocket shuttle and takes you to the 5th world, which is in space.
The last level of Dishonored takes place in Kingsparrow Fort, a military base built on Kingsparrow Island by the corrupt regime, with a giant lighthouse in the center of it.
A lighthouse appears in the Gloomy Galleon area of Donkey Kong 64.
Dragon Quest IV had a haunted lighthouse about halfway through the game. Naturally the ghosts are messing around with the light and making ships crash, and naturally the heroes have to go stop them in order to progress with the game.
In Morrowind the starting town of Seyda Neen has a lighthouse. This is logical because all (official) maritime traffic in and out of Vvardenfell is supposed to pass through Seyda Neen due to, initially, being the location of the Imperial Census and Excise office, and later due to the Blight quarantine. However, other coastal towns, such as Gnaar Mok and Khuul, do not have lighthouses.
In Oblivion, the port city of Anvil has a lighthouse on a peninsula opposite the Countess' castle. It serves little purpose except to provide a gorgeous panoramic view of the city and to hide the gore-strewn Torture Cellar of a rogue Dark Brotherhood Speaker.
Frostflow Lighthouse is an optional dungeon, whose former inhabitants were a group of Determined Homesteaders who didn't realize their would-be homestead was built directly over a Falmer lair...
Another mission has the player get hired by bandits to shut down the Solitude Lighthouse, causing a ship to wreck so they can rob it. When you go to collect your share, they try to pull You Have Outlived Your Usefulness.
In Fable, the Hook Coast lighthouse is situated in an isolated, foggy islet far in the Grim Up North. It's the site of the Hero's battle against his Evil Mentor Maze in the main game, and in the expansion, it's used to call up a Ghost Ship for transport to the Northern Wastes where the Big Bad is regaining his power.
Fallout 3 has a DLC area called Point Lookout. Most of it is a swamp, with a massive lighthouse looking over the coast. The lighthouse itself is on top of the Big Bad's lair. There is also an unmarked quest where you can find a lightbulb and relight the tower.
One lighthouse is actually being lit by a Glowing Ghoul. Once it has been cleared of enemies, it can be used as a Minutemen settlement.
The main game has an unmarked lighthouse in the southeast corner of the map near Poseidon Energy and the Wreck of the FMS Northern Star.
Far Harbor has the Brooks Head Lighthouse, and an unnamed half-sunken lighthouse outside the Invisible Wall west of Huntress Island.
Fallout 76 has a lighthouse the player can visit. It was built purely as a tourist attraction, as there's not a whole lot of maritime traffic in the Appalachian mountains.
Final Fantasy XII gives us the Pharos: the immense, creepy, That One Level lighthouse to end all lighthouses. It's an odd inversion of how lighthouses usually act: In most tales, even the creepiest, oldest lighthouses were once used to guide ships. The Pharos, however, is surrounded in Jagd (which causes airships to plummet) and the seas around the Pharos will sink any ship that gets close. The heroes are also not going to the lighthouse to relight the beacon at the top, but destroy it.
Final Fantasy XIV has the Pharos Sirius, which definitely fits the haunted, creepy part of the aesthetic. It is located on the Isle of Umbra, a dark, creepy island filled with undead. The inside of the lighthouse is filled with all kinds of zombies, with Siren at the top controlling them.
Folklore has one of these. It serves as a bit of a motif for the game.
The Prison section of Ghost Hunter has a lighthouse. Its beam can be seen in most (all?) of the aboveground areas. The boss battle for the level is fought near the lighthouse and its beam is critical for winning it.
Golden Sun has towers called Lighthouses, but they act more like seals on the power of alchemy. However, one can assume that during the times that alchemy is unleashed and the lighthouses are lit, they can actually function as lighthouses, since they're all somewhat close to the sea.
Since Venus Lighthouse is closed to non-Adepts in the first game, Babi is having a new one built next to it, in the hopes that it will allow sailors to keep their bearings on the way to Lemuria.
Grim Fandango had one of these at Rubacava. Not haunted, but it is important and fit in well with the film noir setting, looking similar to a lighthouse on the end of a jetty from the beginning of Mildred Pierce.
Half-Life 2 is the Trope Namer. The lighthouse is not that noteworthy, except for storing a crazy amount of guided missiles.
In the Heroes of Might and Magic series, lighthouses can be found on the world map and grant a bonus to ship movement for whoever controls them.
The "Last Stand" level in Left 4 Dead. It doesn't end well.
In Life Is Strange, there is a lighthouse at the top of a cliff in Arcadia Bay that can be seen in every outdoor scene. Max has recurring visions of watching a tornado destroy the town from the lighthouse cliff.
In Lighthouse: The Dark Being, Sierra's version of a Myst-like game, the titular lighthouse was converted into a laboratory that could create portals to another world.
The Desolation Point map in the winter survival sim The Long Dark is an abandoned coastline dominated by a lighthouse. The lighthouse serves as a good choice for a player safehouse as it has a central location with other key areas (such as the Hibernia Processing whaling facility and the beached fishing trawler) within walking distance, and it gives an excellent view of the surrounding area, as well as having a bed, a fireplace and some supplies, though perhaps lacking in storage space.
Mad Max (2015): Jeet has built his stronghold by an old lighthouse although the stairs to the tower are blocked of by debris. There are several lighthouses occupied by enemies. At least one which is used as a lookout and sniper position.
The original Myst had a half-sunken lighthouse in the Stoneship Age. It was creepy, but what about that Age wasn’t?
There is a lighthouse near Ravenhearst Manor in the Mystery Case Files series. While only a background element in Return to Ravenhearst, later games show us that the lighthouse and the gruesome manor are very closely linked...
Lighthouses are a bit of a motif in Nanashi no Game and on the last day the player character has to climb to the top of one for... some reason.
The Nancy Drew game Danger on Deception Island features the titular island's lighthouse, which has been abandoned and all but condemned for years. Naturally, this being Nancy Drew, you soon discover hidden passageways that link the lighthouse to a network of tunnels used to shanghai unsuspecting citizens in the past.
No One Lives Under The Lighthouse has players take the role of a lighthouse keeper on a remote island, and it quickly becomes clear that there's something out of the ordinary going on.
The entirety of Off Shore is set inside a creepy, abandoned lighthouse at dusk, where your protagonist - an Amnesiac Hero - tries putting the pieces together to how he got there.
Pokémon Gold and Silver has the one in Olivine City, where gym leader Jasmine will be hanging until you fetch some medicine for the ailing Ampharos that kept it lit.
In Professor Layton and the Unwound Future, there is a lighthouse in the middle of the Thames River in future London. The cast comments on how weird it is to build a lighthouse in the middle of the river instead of at the mouth of the river. It's later revealed to be the top of a Humongous Mecha.
The Valix Belt level in Ratchet: Deadlocked is a lighthouse in space, constructed to prevent ships from crashing into an asteroid belt. The lighthouse gets disabled by the game's main villain, forcing Ratchet to reactivate it before it's too late. Not that they'd actually need one.
Ratchet & Clank: All 4 One has a more conventional lighthouse the group runs up the side of while trying to escape a space octopus, which they then fight at the top.
The first level of The Room 3 takes place in a lighthouse named the Pyre, situated on the rocky island of Grey Holm. You have to solve a myriad of complex puzzles to reach the top and light it. Notes from the island's owner state that the rocks are so deadly that the lighthouse wasn't used much.
Saints Row 2 actually has two lighthouses on its map. One near the northern shoreline of the city and one on the prison island. What makes the second especially notable is that it can be bought and turned into a crib for the player and their gang to hang out at. The police apparently don't mind that a high profile gang leader and his crew have set up shop roughly 50 feet from their front door.
Secret of Mana has one, but it's accessed midway through the game, but all it serves for is NPC chatter foreboding of future plot points.
The Secret World features a very large (at the time of its construction, the largest in the world) lighthouse on the eastern coast of the United States. Interestingly, it would be far more useful in the present day (due to the recent fogs covering the region) than at the time of its construction, when it mostly served as an ostentatious symbol to those in the know that the "Enlightened Ones" are here now, and anybody who wanted to evict them from their New World was welcome to try.
Shantae's title character lives in a lighthouse in her hometown.
Shantae (2002) begins with a cannonball crashing through the lighthouse roof.
There's a lighthouse in the resort area of Silent Hill. It's the last of a series of four places to use the Channelling Stone, in order to get the Special Alien Ending.
In Silent Hill: Shattered Memories, "lighthouse" is the last location of the game. It's actually a clinic called "Lighthouse", where Cheryl Mason is treated for psychiatric disorder caused by loss of her father.
Sonic Adventure has one in Emerald Coast. In Sonic's section, Sonic comes to the lighthouse just after evading an orca that rips the dock he runs across apart, and the cave near it forms the second part of his section. In Big's section, Big has to fish for Froggy, his pet frog, who is swimming near the lighthouse.
The fella tending the one in the second chapter of StarTropics directs you to his wife a little further east, who in turn tells you of the bottle containing the code to switch on the sub's dive function.
Lighthouses appear scattered throughout the Unterzee in Sunless Sea, and sailing in their lightbeams helps reducing Terror. One of the, the Ragged Crow, is run from the Undercrow, and the waters surrounding it are haunted by the dreaded Tyrant-Moths, which are attracted to its lightbeam.
The Mario Kart DS track Cheep Cheep Beach features a lighthouse.
In Mario Kart 8, the Cheep Cheep Beach lightouse reappears. The track Bone-Dry Dunes also has lighthouses that oversee the sand rivers.
Among the Violet Islands in Paper Mario: Color Splash is Lighthouse Island, which as one might expect prominently features a lighthouse. Its lights are out, and as such an entire portion of the sea is pitch black (despite being in broad daylight).
Tales of Symphonia has one in PortParadiso. It's of note because characters mention that you'd better not go near it, but the quest surrounding it suffered a case of Dummied Out.
A memorable example in Thief II: The Metal Age; the whole first floor was an elevator to the secret underground steam-robot base built into the ruins of a pirate hideout.
To the Moon has Anya, the lighthouse behind Eva and Neils client's house. River, the wife of their client, Johnny, was very attached the lighthouse, but Johnny never understood why.
Fixing the lighthouses of Britannia is one of the few Side Quests that still work in Ultima IX.
The Witness: Interestingly, even though the game takes place in an island full of buildings, there's no lighthouse to be found. However, a peninsula in the southernmost section of the island features a ruined structure that is widely speculated to be a former lighthouse, considering its location (in a secluded peninsula which happens to be very close to the town).
