In The Legend of Zelda: Ocarina of Time, for example, Gohma doesn't appear until you look up at the ceiling, Volvagia won't appear until you jump to the main platform, Phantom Ganon won't appear until you try to leave the room, Dark Link doesn't appear until you turn around, Morpha doesn't reveal itself until you swim to the center platform, etc. (However, before the door closes behind you in Gohma's room, you can look up and see her, vaguely, and it will not trigger the battle.) Majora's Mask contains a particularly unique example in Goht, who is plain sight the moment Link walks into the Boss Room, but is frozen solid and must be hit with a fire arrow to be awakened— at which point he promptly tramples you and runs off.
In Minish Cap, the boss of the Temple of Droplets is an ordinary Octorok which has been frozen, as has the element of water. You can see it sticking out of the wall soon after entering the dungeon, but you cannot face it until you unfreeze it, along with the element, much later on.
And Morpheel, who looks exactly like Morpha from Ocarina of Time at the start.
If mini-bosses count, then the Deku toad from Twilight Princess is the straightest example. You surface in the boss arena, and in true ZeldaGhost Butler form, the hole seals itself behind you. He will not drop down and start the fight until you go into eye-camera mode (c button on Wii) and scan the ceiling for him.
Also a mini-boss, Wart (Giant eye surrounded with bubbles) from Majora's Mask also does this trick. It will not attack until you go into first-person mode and look up at the very, very high ceiling. Once you make eye contact, it will drop to the floor and begin trying to ram you.
The mini-boss in Twilight Princess's Arbiter's Grounds doesn't show up until you cut one of the ropes holding its sword. You can't actually see the boss until you activate your wolf senses.
The Legend of Zelda: A Link to the Past has Blind the Thief, the boss of one of the Dark World's dungeons. While exploring his dungeon, there appears to be a room with absolutely no purpose at all, but upon exploring the dungeon some more (rescuing one of the seven maidens that are sealed in each dungeon and blowing up some floors on the level above in the process), you can return and discover that the "maiden" is actually Blind himself, who is forced to reveal himself by the bright light (which is his weakness) that now shines in the room (thanks to the aforementioned floor bombing). Cue boss fight.
The boss of the Face Shrine in Link's Awakening does this. Walk into a room. Empty. Giant face on the floor which will kill you. Boss.
That would be Facade. For extra fun, he returns as a mini-boss in Snake's Remains, the second dungeon of Oracle of Seasons, and then again at Onox's Castle. Because fighting a demonic-looking disembodied face once wasn't bad enough.
Slime Eyes, boss of the Key Cavern is hidden and drops Mooks from the ceiling until you dash into a wall and dislodge him, causing him to drop into sight. If you don't pick up on the hint to use the Pegasus Boots and ram the walls, he'll eventually drop down of his own volition.
Phantom Hourglass also has the Boss on the ghost ship that won't show up until you get all four of the "sisters" together. Justified in that the sisters themselves are the boss.
Multiple colossi in Shadow of the Colossus. Often they will appear to be nothing but a pile of ruins, but will begin to form when you approach them. One of the underwater colossi doesn't appear until after you swim around for a little while.
The Queen in Ico, who doesn't appear until you try to leave the apparently-empty throne room.
Castlevania: Portrait of Ruin has a rare example of He Was Right There All Alongthe level: in the "Nation of Fools" portrait, you can see in some sections of the level a huge spherical object darkening the background, and when you grab an important object on a small room he comes forth, revealing himself to be the well-known boss Legion.
Dawn of Sorrow had the appropriately named boss, Paranoia, who won't appear until Soma walks in front of a mirror in the middle of the room.
Then in a later boss fight against Dario Bossi, a large demon can be seen in Dario's reflection in a mirror during the fight. Continuing to attack Dario will lead to a bad ending. However, using Paranoia's soul to enter the mirror behind the apparent boss, you get to fight the demon Aguni.
Legacy of Kain: Soul Reaver has Dumah, the fifth boss, who has already been killed once by a pack of vampire hunters and impaled with six-foot stakes to his own throne. Of course, being a vampire, he can be brought back to life in an instant by pulling the stakes back out, and players can square off against his spirit in the game's Spectral Realm.
Beyond Good & Evil has a particularly impressive sequence where you enter a room over a strangely organic-looking bridge, then photograph a cute pair of one-eyed creatures. Then the boss retracts its tail which you just walked over and eyestalks which you just photographed.
Also done with both bosses in the second dungeon. The first one appears in the central part of the level (which you're bound to go back and forth through a few times), but not until you've gone and saved Double H. The second one's found in a room you can see the room long before you can get to it, and even when you do, the boss doesn't appear until you look around the room in camera mode.
Cave Story. Monster X allows you to walk right past it before it activates and begins attacking. The Core is inert while you explore its chamber, and only becomes active at the end of a cutscene that you trigger by speaking with Curly.
Several bosses in Ys I and II don't spawn until you try to open the treasure chest in the room.
In Ys III, a statue in a bubble blocks your path in Valestine Castle, and you must find the Plot Coupon to make it disappear. Later, it returns as a boss.
In Enslaved: Odyssey to the West, there's a section where Monkey, Trip and Pigsy are looking for parts to repair Pigsy's flying craft. The last part they need is a power cell, which they find sitting out in an open area, otherwise occupied only by large piles of junked machinery. Monkey and Pigsy have a brief discussion about how lucky they are to just find it sitting there, Monkey clearly not believing the group's apparent luck. Only after Monkey jumps down into the area and gets the cell does Pigsy warn him to "watch out for the Rhino." Monkey doesn't know what he's talking about - until one of the junk piles shifts, and a huge mech emerges from it.
Dark Souls has the Continual Discharge, a giant demon that is the source of the molten pools just after leaving Quelaag's Domain, and you can enter the arena, and have to pass by it and pick up a set of armor and turn around before the demon will even think of trying to attack you.
Sort-of subverted in NES game Monster Party with the Giant Spider he's there, looking like he might be waiting, but in fact he's already dead.
In one stage of Unreal, a giant statue of a Titan is seen sitting on a throne. When you grab the upgrade sitting on the conspicuous button, the statue stands up... It's the first time you see a Stone Titan which is basically a normal Titan with a different texture and an extra helping of HP.
Another example is the Warlord. When you enter the lava-filled cave, the boss is facing the other way and only gets alerted when you get closer.
Played straight in Doom 3. You walk through a doorway into a seemingly empty arena, before finding out you just walked under the Cyberdemon's legs. Either it just likes to stand over doorways and freak people out or the door spontaneously changed its destination. (Hell is weird like that.)
Resistance 2 features the Mother Spinner, who you don't see on the top of the tower in Twin Falls, Idaho until you look directly up the girders and then the battle begins.
Some bosses in the Descent series do this, for example the first boss of II is initially hidden behind a disappearing wall. The second boss doesn't activate until it directly sees you or you hit it.
The Giant Eye Of Doom (Golden Eye) in Turok 2. You walk into a large supposedly-empty cavern, then look up to see the eye gazing at you.
The final map of the first part of Quake has Chthon, a Puzzle Boss. You can go anywhere on the map and do anything but he won't appear until you grab the Rune next to the lava pool. Cue giant lava monster rising out of the pool...
The Lurker Below in World of Warcraft has to be fished from the water before your group of heroes can fight it - this is usually pretty hilarious, as twenty-five players stand around buffed to the gills while someone fishes.
Sapphiron is probably a better example. You walk into what sure looks like an empty room with naught but a few bones laying about. They may as well have put up a neon sign screaming TRAP!!.
Dark Falz, in Phantasy Star Online. It's an obvious trap of course; after slogging through the hell that is the Ruins, you enter a sunny meadow chamber with a monolith in the middle, all sunny and cheerful and peaceful with calming music. You walk up to it and interact with the altar near the monolith... suddenly everything goes hellish and a droning sound starts as hundreds of bladed things come after you. Then Dark Falz shows up!
Lampshaded in Voodoo Vince, in which Vince enters a large room and sees nothing but a pile of bones. He wonders aloud where the boss is, and as he says it the bones begin to form into the boss of the level.
The Metroid series loves this one. Let us count the ways:
In Metroid Prime, both of the bosses in Phendrana Drifts wait for you to try and grab their power-up before they attack. Later, in the Phazon Mines, the Elite Pirates (and the Omega Pirate) won't wake up until you approach their stasis tubes. The Phazon Elite won't do anything unless you blow up the tube he's held in.
The Chykka boss in Metroid Prime 2: Echoes won't attack until you shoot its cocoon and drop it into the water. In the same area, the Alpha Blogg mercifully can't reach you until you've visited the room just beyond it. Finally, the Ingsmasher waits in a storage rack until you approach, just like the Elite Pirates. There's also the Alpha Splinter, Alpha Sandigger, Dark Missile Trooper, Amorbis, Quadraxis (you already saw him dismantled in the light version of his room), Boost Guardian, Spider Guardian... Hell, it's quicker to list Prime 2 bosses that don't do this.
The Jump Guardian in Prime 2 actually inverts this; as you enter the room, he's right where he'll be when the cutscene starts. He's invisible, but you can still hit him.
In Metroid Zero Mission (which is actually a remake of the original game), the Acid Worm won't pop out until you zipline across the room. Similarly, Ridley waits before divebombing from the ceiling until you've entered the room behind his lair, retrieved the (temporarily unusable) power-up, re-entered his room, walked to the far door to see that it wouldn't open, and turned back around.
In Super Metroid, the Torizo boss is a Chozo statue which won't attack until you take its item and try to leave the room. One of the X-Parasites in Metroid Fusion tries the same trick, but you can see it coming a mile away because it's the only Chozo statue in a Federation-built science lab.
Or, if you didn't already catch that one, you can shoot at it (in an attempt to reveal the power-up, like in the other games with Chozo Statues, which is probably what they wanted you to do).
Also in Metroid: Fusion, the first time you leave Sector 5, you see a large shadow dashing through the background, accompanied by a loud noise and screen-shaking. Much later in the game, you are sent back only to find out what's really been there all along is a giant, grotesque boss, aptly named "the Nightmare."
The Ridley battles from Super. "Oh, there's the Metroid hatchling... I guess there was nothing to worry about afte—OH HOLY CRAP"
Nearly every single boss example in Super Mario Galaxy has the boss invisible or out of view until the battle begins with only about 4 examples in the entire game being in sight beforehand.
Also in the sequel, there's a boss that's disguised as a planet!
Bigger Boo in Yoshi's Island starts off just beyond the far edge of the room. Like all Boos, he can't move onto the screen until Yoshi is turned away from him.
All other bosses usually subvert it by waiting already. Amusingly, by refusing to follow this trope the letter, it's actually possible to defeat the giant Piranha plant boss of World 3 before the battle starts. Kamek then flies in and the reaction on the ordeal is priceless.
Used rather weirdly in Rayman Revolution. When pursuing the second Mask, you find yourself in a room with a big statue. Of course, as every one who doesn't suffer from acute Genre Blindness would guess, when activated, this statue is Umber, the Guardian of the Mask. It gets weird when Umber not only does absolutely squat to guard the mask but also provides you with transportation along deadly lava to where it's being kept.
The Hulking Lungfish boss in Psychonauts doesn't immediately appear when you enter its arena. You get to wander around in the air bubble on the lakebed for a while before it appears.
The boss of the first area of Jackie Chan's Action Kung Fu is a Buddha-like statue that becomes alive when you scroll fully into the room. The boss of the third area is a toad that suddenly transforms into a huge flying fire-breathing toad, and the boss of the fourth level is a suspicious cloud that transforms into a huge purple cloudy cyclops.
Targitzan in Banjo-Tooie — you walk into his "Really Sacred Chamber" and see a Jiggy in the middle of the floor, and as you approach it he leaps out of the floor.
And Old King Coal of the same game... and the Patchy Dinosaur fellow... and about every third boss from both games, really.
Mad Jack, the boss of Frantic Factory in Donkey Kong 64. You can actually look up at the ceiling and see the boss hiding in a hole, but he won't move. There are sixteen short platforms on the floor, and you have to step on the one with the light flashing over it. Only then will the platforms rise several stories into the air and the creepy evil robot jack-in-the-box duck thing come down to fight you.
The boss of the Mausoleum of the Giants in La-Mulana is a robot disguised as one of the giant statues in the background.
At least three Maverick Reploids in Mega Man X were right there: Sting Chameleon (active camouflage), Spark Mandrill (fade to black, his light bulbs light up, and then the lights return), and Boomer Kuwanger (fades in ninja-like). The wall-face Rangda Bangda was also right there.
Averted in I Wanna Be the Guy, where the moon, which has been in the background for much of the game, drops out of the sky as if it's a boss. A moment later the real boss kicks it aside.
At the end of Mushroom Hill Zone Act 2 in Sonic & Knuckles, you find a radar dish, destroy it, then Robotnik's Eggmobile emerges from beneath it. In Flying Battery Zone Act 1, you find what appears to be a Prison Egg, but then a pair of Epic Flails pops out and attempts to smash you.
Pikmin has the Beady Longlegs, who drop down on you. The Titan Dweevil, Snagret, and Emperor Bulblax all come up from underground. Also the source of the page image.
Another such enemy in Pikmin 2 is the creeping chrysanthemum. It looks like a lot of the normal flowers that are all over the game except it has narrow blinking eyes staring at you which are hard to notice. If you approach it, it pops out of the ground & reveals the giant fat root that is its torso. It uses its stem arms to scoot around on its "butt" & tries to eat your Pikmin with its red flower mouth. If you or your Pikmin are too close to it when it initially pops out of the ground, you'll get knocked over making it extra hard to avoid losing Pikmin.
In Magus's Castle in Chrono Trigger, the party comes across an easy monster they believe to be the sorcerer Flea, who dies quickly. Then the bat which followed them for the entire time reveals himself to be the real Flea.
Ditto for Shadow Hearts, where the cute doggy following you through Chapter Nine turns out to be the aptly-named Beast Dog.
Also parodied in the new Bard's Tale, where a giant undead viking lies dormant, waiting for you to approach his throne before attacking you. However the Bard, being extremely Genre Savvy, calls him out on it, and refuses to move forward until said undead berserker wakes up from afar.
The second Bard's Tale game from the original trilogy had this as well. The Big Bad Lagoth Zanta is actually the hermit sage that offers advice throughout the game.
Mega Man Legends has a room with a strange yellow column in the middle. You bypass it and move on. When you go through the room again on your way back after finding the Plot Coupon, arms, legs, and a head pop out and you have to fight it.
In Kingdom Hearts II in the basement of Beast's Castle , you enter an empty room with a stone door carved with a gaudy double-gargoyle thing with its "arms" guarding the handle. Donald walks up to the handle... and the "decoration" takes a swing at him. Cue boss music.
Final Fantasy VII has Gi Nattak, who is nothing but a frightening mural on the wall when you enter the room that he is in, but after a short conversation, the mural suddenly comes to life.
Another example in the same game (and really every Final Fantasy that features this monster) is Demon's Gate, who starts out as simply a creepy wall with audible heartbeats, but later appears through said wall and attacks.
Final Fantasy IV had one dungeon with quite a few mini-bosses called "Trap Doors" they look exactly like regular doors so you won't know which are safe. They are very tough, and like to use unavoidable 1-hit KO's on your party members. The most annoying thing about them is that 70% of them lead to empty rooms, thus wasting your time.
The World Ends with You features a boss during the third week who hides in Beat's shadow for most of a week, and she's supposed to be that week's GM!. Really was there all along.
This occurs anytime you encounter a Thresher Maw in Mass Effect, primarily in the mission where you're searching for Admiral Kahoku's missing marines. It doesn't appear until you drive really close to the Marines' vehicle, which is sitting right on top of a Thresher nest.
Monster Hunter has Basarios, a relatively small boss monster with a layer of rocks over its body. It has a big clump of rocks on its back, and when it hides underground this part sticks out, looking like any other cluster of rocks you'll see on the volcanic belt.
Similar to Gobul above, the ridges on Nibelsnarf's back resemble the mounds of sand that only appear in the desert in missions that involve it.
Done in a weird way in Wild ARMs. In a volcano dungeon, our heroes enter a small room with a dead end and an odd tapping noise coming from one of the walls. After wondering aloud what to do, the tapping stops, and Zedsmashes through the wall and challenges you to a duel. Afterwards, he leaves and you continue through the hole he made.
Fallout 3: You discover a teddy bear in a shopping cart cage in the Jury Street Metro trainyard. Opening the cage causes the bear to wave its arms, still nothing special happening. But then, a Super Mutant Behemoth appears out of the east to clobber you.
The obscure shooter Metal Black has an "all along the level" version with a literal That's No Moon: you can see the satellite right from the beginning of the second level, only to see the true one at the end of it. At this point the fake moon draws closer and cracks up, revealing the boss inside.
At the end of the final planet of Super Stardust HD you get the regular 'Boss Incoming' countdown. Then the planet explodes, revealing the boss to have been in its core all along.
In one level of R-Type FINAL, your ship slinks through a gargantuan biometrics lab cycling around an equally huge stasis chamber. From time to time you get a glimpse of the creature in the tube, who bears a resemblance to one of the game's most famous recurring bosses, Dobkeratops. No further explanation should be necessary.
G-Darius has Zone Nu, "Genesis". During the level, you see a large tetrahedron being formed as you revolve around it. After fighting through a slew of enemies, the tetrahedron suddenly morphs into an armed form. It turns out to be the boss, The Embryon.
The fourth chapter of Ikaruga is set in and around a satellite-like structure, which turns out to be the stage boss itself.
The second level of EDF: Earth Defense Force turns into a subverted Battleship Raid halfway through. After blasting your way through the turrets and several smaller aircraft, the level's true boss blasts its way out of the front end of the carrier.
In the third stage of Lightning Fighters, you encounter several battleship-type watercraft, then they all merge together to form the stage boss. In the first stage, the boss flies overhead a couple times before you fight it.
When you meet the Garrador of Resident Evil 4, he's chained to a wall and covered with invulnerable armour. To escape the room, you need to get right up into the guy's hairy mutated grill in the hope of pulling the switch that opens the door. He waits till you're six inches away before breaking out of his chains and beginning the battle.
Earlier, you pass by a locked gate that you can hear something growling behind. When you return to this area at night, that something is revealed to be El Gigante. Cue boss fight.
Mendez pulls this on Leon when you enter the warehouse where you fight him.
Also occurs with Verdugo. First he's shown stalking you from Jaws First Person Perspective, then he periodically claws at you from the ceiling; only after you activate the elevator power and attempt to open the shutter does he drop down and fight you face to face.
The Resident Evil remake for the GameCube makes a damn fine scare out of this. You open a door and walk into an empty room... and then the door swings shut behind you and you see the giant fucking spider that was clinging to the back of the door all along oh God.
Also in the REmake, the first encounter with Lisa Trevor in her cabin. Whilst there is the sound of the door opening to warn you, you had no idea she was around the cabin before that.
In Resident Evil 2's B scenario, you come to a security room, turn on the monitor, to find that Trenchcoat Tyrant is right behind you, and he promptly smashes the camera.
In Resident Evil 3: Nemesis, Nemesis does this a few times. In fact, one of the game's selling points is that Nemesis can literally attack from anywhere.
Silent Hill: You enter the boiler room of the Evil School, you hear footsteps and heavy breathing, then you turn around to see the Split-headed Lizard monster. In the second game, you enter a hallway in the alternate hospital basement, then after taking a few steps forward, the camera shifts to reveal Pyramid Head right behind you.
Likewise in Transformers: War for Cybertron, where Megatron's space station, which you were assaulting in the first place, turns out to be Trypticon. In a twist, instead of transforming on his own, you have to infiltrate further than planned and force him to convert into robot mode before a proper confrontation can occur.
The first phase of P.N.03's Final Boss battle is a robotic skull-looking thing. After you inflict a few hits on that, the boss's true form drops from the ceiling.
In the third level of Syphon Filter: The Omega Strain, Masson, the ALA terrorist leader, can be heard shooting and will kill the SWAT officers if you don't get them to safety, but he doesn't physically appear until you complete all the objectives.
Rise Matsumoto of Yuru-Yuri doesn't formally get introduced till episode 9 of Season 1 in the anime. But when she does show up, they are really surprised to see her and that she's the Student Council President. One of the other characters mentions that she was always with them, but just slightly off-screen. Cue a flashback scene that then veers slightly to the side to reveal she was with them in that picture.
Sword Art Online: High-Floor Bosses tend to favour this, particularly The Skull Reaper, which drops from the ceiling and insta-kills two members of the clearing team.
In Cat Paradise, it turns out that Akitaka Sandou, the Bigger Bad, the person behind most of the plot, the founder of the academy where the manga takes place, and someone who was also thought to be long dead, was actually hiding amidst Tsukomoisshu's severed head collection for almost the entire story.
In the Leslie Nielsen film Spy Hard, the Director of the CIA often happens to be blended in with the surroundings, whether this entails becoming a leather armchair or disguising himself as the painting of George Washington on the wall.
Alien: Brett moves through an empty room with machinery and chains hanging from the ceiling. After he moves off, the monster moves in the background, revealing that it was just camouflaged in plain sight the whole time. It happens to Ripley, on board the Narcissus, where the Alien is hidden in plain sight among the wall detail and then suddenly uncurls to the horror of Ripley. The Xenomorphs make something of a habit of this, it happens in almost every film.
This is actually subverted in ''Alienł where Ripley believes she sees the xenomorph lurking in the shadows, but it turns out to be just a bit of piping in the shape of the creature's head.
In Indiana Jones and the Temple of Doom, Indy's bedroom in the palace has an elaborate mural decorating the walls. As Indy stands around waiting for Willie to arrive, one of the figures steps away from the wall behind him, revealing himself to be an assassin.
In Pan's Labyrinth, when Ofelia first enters the well in the middle of the titular Labyrinth, the Faun can be seen in the background for the whole scene before he declares himself, but his wood-like body blends in with the other debris so well that the viewer is unlikely to notice him until he moves.
Similar to the Indiana Jones example above, Wild Wild West has a painting of a man with a rifle, which turns out to actually be a man with a rifle, well camouflaged until he moves.
Meta example. Who turned out to be the real Big Bad in Tensou Sentai Goseiger? Warstar? No. The Yuumajuu? Nope. The Matrintis? Uh-uh. It's Bladerun, the villain who was a part of every single one of those organizations.
Spaced: Tim is sitting on a park bench, apparently talking to himself. Then Mike pops out of the bush he's disguised himself as. In another episode, Daisy enters Brian's apartment looking for him. He doesn't appear to be home, but as she leaves, we see Brian covered in paint and blending in with a canvas.
Anything involving Granny Weatherwax of Discworld. Also Vetinari, who at the Assassin's School was always marked absent in stealth class...
Death, and through him Susan and presumably Mort as well, have the ability to appear as part of the background, same as Granny Weatherwax (although presumably he came up with it first). In all cases the person using the ability in question is described as being there, but the eye doesn't really see them as a person until they reveal themselves.
There's a scene in Guards! Guards! when the dragon pulls this. The Watch is nervously scanning the city skyline at night, waiting for the dragon to show up. Then one of them asks if that tower has always looked like it has a dragon clinging to it...
Just before facing down Inheritance series Galbatorix in his throne room, the Heroes see a massive sheet of black in the back of the chamber, which they believe to simply be a mountain sized curtain. It moves aside, being just a fold in the wing of his dragon, Shruikan.
Necron lore in the fourth edition of Warhammer 40,000 tends to involve this. In its most basic form, the aptly-named Necron Tombs appear to be just that — incredibly large and elaborate, with advanced technology strewn everywhere, but not a living thing in sight. And then some damn fool, usually a techpriest, gets the urge to fiddle with things and the Necrons themselves show up, often by teleportation, and proceed to slaughter everyone.
The Chief in Inspector Gadget always appears by popping out of some random object he happens to be disguised as in the background. Unfortunately he usually disguises himself as a trash can, which Gadget unthinkingly disposes the exploding message into after their conversation...
In T.U.F.F. Puppy, The Chameleon, being a shapeshifter tends to spy on the heroes while being disguised as some mundane object.