The Legend of Zelda games can be a weird case of this. Check the map. You're standing in front of a door leading to a round room with no other exits. Yes, the door is going to slam shut behind you and you are going to have to face a Boss Battle. On the one hand, the door slamming shut won't surprise you, but on the other hand, if you're the squeamish type, you'll be shaking in anticipation of the unknown boss fight.
Happens in pretty much any game with a map and boss battles. If you see a large room with 1-2 exits, it's safe to assume there's a boss fight there.
Well keep in mind that all games that give you a map tell you that THE BOSS IS HERE, usually with a skull on the 5th floor or basement.
Not so much, however, for the Sub Boss of nearly every dungeon.
Inverted in The Legend of Zelda: Majora's Mask, where the area leading up to the final boss is a peaceful green field with a large tree in the middle of it. Of course, to get there you had to be eaten by the Moon, which is possibly the most foreboding thing in the entire damn series.
Similarly, the Castlevania series actually has the doors leading to boss fights look and act entirely differently from doors anywhere else.
The Metroid Prime series (hell, possibly the whole series) has the hint referenced above.
Metroid Games love putting giant eyes over boss doors, complete with Eye Beams. Basically, if you see an eye ontop of a door shooting lasers at you, there's a boss in that room.
In Cave Story, all of the sand pits in the Outer Wall contain Sand Crocs. So, don't step in the sand.
In general, after the Sand Zone, players are a lot more cautious about sand.
Uncharted: Drake's Fortune. You know there're going to be baddies up ahead if you encounter conveniently placed objects that serve as cover, usually low stone walls or crates.
The same applies to most cover-based games, such as Gears of War and Mass Effect- contrary to what most players will be used to, if you're in a wide open arena you're probably safe. If you see lots of waist-high obstructions, expect trouble.
From Zero Punctuation: "Another thing that characterizes the Gears of War universe is chest-high walls. The two opposing armies have both realized that chest-high walls are the key to victory. Every single battleground is littered with chest-high walls, everyone's bombs seem specifically designed to reduce buildings to chest-high walls, the Locusts have developed technology to make chest-high walls rise out of the ground, and if all else fails Mother Nature herself will step in and make rocks fall from the ceiling forming chest-high walls!"
Several bosses in La-Mulana can be found in dead-ends with unique-looking architecture that seem pretty useless...that is until you've fulfilled some obscure requirements and have at least one Ankh Jewel, at which point an Ankh will appear in that room and the music will change.
Young Merlin on the SNES. In the final portion of the game, you will arrive at certain rooms containing bosses connected by a ridiculous minecart...boarding section. Not only do the doors look different, but the some of the rooms themselves contain large black flags with red bleeding eye symbols painted on them. Not foreboding in the slightest!
Lampshaded at one point in Enslaved: Odyssey to the West. The power cell the characters are looking for is in the middle of a big boss-type arena with health and ammo littered all around and they're rightly suspicious of it. Then the boss charges in.
First Person Shooter
In the Half-Life series, if you're in a dark enclosed space, there is usually going to be a headcrab. If it's dark space with a high ceiling, it's going to be a barnacle. And if you're in water, there will be either those killer shrimps or a swimming dinosaur.
In Half-Life 2, with such a focus on their physics engine, big fights can be pre-empted by masses of saws, exploding barrels and cinderblocks.
According to the commentary for Episode One, beta testers will occasionly recognise the signs of a headcrab nest (dark, small room, no windows, hey what's that in the corner...) and be so pre-emptively frightened that they'll simply stand outside and use all their ammo to incinerate the room, instead of entering and killing the crab with one shot.
In Doom, dark areas usually mean that the Spectre demon will show up, as it is hard to see. Large open spaces practically mean arenas with humongous demonic armies teleporting in. Long hallways mean quickly opening monster compartments behind the walls. Large lifts (preferably with a pillar in the center) mean it's going to be a slow/long and painful way down as monsters shoot you from alcoves, or get up close and personal by teleporting in. And these are but a few...
In Clive Barker's Jericho You can bet your supernatural arse that that a monster is going to jump out of a pool of gibs as soon as you get near it. Every. Single. Time.
Small alcoves in Serious Sam are usually a sign of an incoming marsh hopper wave.
The original Wolfenstein 3D is the GRANDDADDY of of Foreboding Architecture... Between Hitler and other Nazi themed wall panels there was always a hideout or treasure trove nearby, or behind.
Played with in Left 4 Dead. The enemies are randomized, so you're basically hoping and praying that a Tank doesn't show up when you're in a tight area, or a Charger when you're on a high area with no guard railings.
In the game F.E.A.R, if you see a small room whit no lights, be sure that there will be a replica assassin (an invisible melee enemy) inside, waiting on a corner on the ceiling. be carefull whit the elevators, too.
In Blood, if it's ground, prepare for zombies climbing out of it. If it's a gargoyle statue, prepare for it coming to life. If it's a small hole or a passageway too low for you to fit even when crouching, prepare for rats, spiders or, worse, Hell Hands to emerge from it. If it's water, there will be Bone Eels and Gill Beasts. If it's dark, prepare for phantasms. If it's neither of the above, Cultists and Fanatics are waiting for you.
Borderlands and Borderlands2 are full of this; wander in to a ramshackle of scrap metal with skulls everywhere? Bandits are about to start pouring out.
Practically every narrow ledge in Banjo-Tooie requiring the Grip Grab to traverse will have a Snapdragon leap out and attack you.
All of the Bowser levels from Super Mario Galaxy end with green checkered stairs that get smashed away by meteorites before the boss battle against Bowser.
The original Super Mario Bros. has Bowser's fire flying past you to show that you are almost near a (fake, or in the final level's case, real) Bowser at the end.
In Time Stalkers if there's a wide open room on the map you'd better believe that it's the last dungeon level boss fight.
Role Playing Game
The Chrysler Building in Parasite Eve. All of the building is made up of narrow hallways, but when you approach a large room and the music suddenly stops, you know a boss is right there.
Generally, this trope is rarer in Role Playing Games, where boss fights are often telegraphed by lengthyconversation and battles take place in a pocket dimension. But in Baldur's Gate, one room on the third floor of a dungeon seems suspiciously large. The player slowly creeps into this too-wide and too-tall cave, anticipation mounting, when, all of a sudden, MASSIVE DRAGONOUT OF NOWHERE.
Even better, other than the Shadow Dragon, every dragon's lair in 2 and Throne of Bhaal has pretty much the exact same architecture: a long staircase from the upper-left/right of the map, leading down into a massive, dead-end hallway with pillars on the sides.
In The Dark Spire, the appearance of the surrounding area will drastically change a few steps before the Final Boss assuming you're using the Modern display mode.
The combat system of Anachronox requires that most battles take place in large, squarish, completely empty regions of floor which stand out against the generally narrow hallways, making these plazas as foreboding as the space monsters invariably hanging out in the middle of them. Subverted in one area, with a tentacled monster waiting for you in just such a plaza. Turns out he's a vegetarian, and he just wants to swap recipes.
You are playing Mass Effect 2. You have just walked through a winding hallway and are about to enter a very large room with plenty of chest-high walls. What do you do? If your answer isn't send your squad to hiding position and start hitting any preparatory powers before taking a storm-speed dash for the closest wall, you've not been playing for very long.
Though it's subverted with the Collector Vessel mission. The ship is filled to the brim with conveniently-placed chest-high walls...but there are no enemies. It's far creepier than it sounds. The enemies don't come out until after you try to leave.
In The Elder Scrolls series the type of a dungeon usually indicates which kind of enemies you will encounter, but not always. For example, dwemer ruins contain automatons, daedric ruins contain daedra, crypts/catacombs contain undead etc. Usually the more important a quest is the more likely this trope is averted.
Although Thief: Deadly Shadows is pretty much completely filled with foreboding architecture (and music) I think we all knew, as soon as we started Robbing the Cradle, that this was going to be unpleasant. (Though we could not have anticipated how scary it really was.)
Monsters love to crash through windows in the Resident Evil series. In RE 2, when you are forced to enter the suspect-side of a one-way mirrored interrogation room, everyone knew what was coming next. When Capcom released the Gamecube Remake of Resident Evil, one of the more effective scares was triggering the zombie dogs to crash through the windows much later in the game, when people had become complacent.
Wide Open Sandbox
Minecraft has this for its dungeons. Do you see a wall of cobblestone or moss cobblestone within a cave? That's a dungeon with a spawner ready to spit out monsters when you approach it.