Played with in Pokémon HeartGold/SoulSilver, where you have to infiltrate Team Rocket's activities at the Goldenrod Radio Tower by donning their uniform. Hilariously, the same Mook who just shoved you away from the door gives you a cursory look, then allows you to pass. Especially funny when you consider that all Rocket Grunts look alike, probablly they don't have eleven-year-olds in their ranks, and generally aren't sporting pigtails, if you're a female player.
Made better when your rival comes in, recognizes you immediately, wonders what's up with the disguise, and strips you of it, then to have the grunt finally recognize you.
Speaking of which, a variation involving inanimate objects was also used. The transmitter used to cause the Gyarados to evolve at a rapid rate at Lake of Rage (and was implied to be the cause of the Red Gyarados) was disguised as a tree near the shop. "Disguised" meaning rather obviously (the control box was clearly seen, not to mention most of the "tree" was metallic gray).
The "Ninja" class of Trainers in Pokemon Sapphire/Ruby/Emerald are often disguised as scenery until you pass into their range. However, it's usually a tarp with a painting of the scenery (usually a tree). Some were disguised better than others; for instance, those who hid in sand mounds looked indistinguishable from regular sand mounds.
Sudowoodo is a tree mimic (it's not a Grass-type at all) who tries to pass as an ordinary tree, and usually stands out if you pay any inkling of attention. In Pokémon X and Y, you can run into hordes of Trevenant (which are actual haunted trees) with a single Sudowoodo trying to pass itself off as being part of the horde.
Played straight in every game of the Hitman series, where 47 can get away with some rather ridiculous disguises (Six foot white guy dressed as a Chinese triad member, anyone?). However, this is averted on harder difficulty settings where most "disguises" won't be all that effective, even against mooks.
In Sonic Adventure 2, a hedgehog named Shadow steals a Chaos Emerald from Station Square, and despite having black fur with red highlights as well as a different spike style, the military thinks it is Sonic and charges him for the crime.
Later in the game, even Amy, who is deeply obsessed and in love with Sonic, mistakes Shadow for Sonic.
In Paper Mario: The Thousand-Year Door, one of the members on the sailing crew you join up with is obviously Lord Crump, The Dragon to the head of the X-Nauts. Although no one notices, Crump himself admits that his disguise is pretty bad, and in an aside he does ask the person 'behind the TV' not to tell Mario his real identity or else, also lampshading the ridiculousness of the disguise in the process. Since every character in the game is two-dimensional (as in, physically), this is quite literally a Paper-Thin Disguise.
Additionally, Mario can "disguise" as Luigi by wearing the L Badge. All this does is Palette Swap his clothes to green, but it's still enough for a self-proclaimed Luigi fan to mistake Mario for the real thing, to the point that when the real Luigi suddenly shows up the fan accuses him of being an imposter. It seems Luigi can never get any respect.
On an unrealated note, Mario can also use the W Badge to "disguise" himself as Wario, or use both the W Badge and L Badge at the same time to "disguise" himself as Waluigi. Neither effect has any practical use (there's no quest that requires either). In fact, you can only get the W Badge from Charlieton (note the name), a merchant who sells a mixed bag of items (most are overpriced junk, but he does have a few useful things).
In Super Paper Mario, Nastasia dresses Luigi in black clothes and provides him with a mask, so his brother won't find out that Mr. L is really Brainwashed and Crazy Luigi. However, he keeps his hat, his mustache, his way of moving, his shoes.... virtually everything about him is shouting: "HEY, I'M-A LUIGI IN-A A BADASS-COSTUME-A!!!" Naturally, none of the other main characters - not even his own twin brother - manages to recognize him in this getup.
In Super Mario Sunshine, Shadow Mario commits vandalism on Isle Delfino and the Piantas believe Mario to be the culprit, as despite the fact that Shadow Mario is totally blue with a watery texture he had to be Mario.
In Paper Mario 64, the Koopa Bros. boss fight start off piloting a boxy, conspicuously fake disguise of Bowser. The four Koopa Troopas inside converse with each other loudly enough for Mario to overhear while in disguise, which doesn't help much, either.
In Hotel Mario, Iggy wears a comically oversized Bowser mask (and nothing else to disguise himself) during his battle.
Super Mario 3D World features a power-up that disguises the character as a Goomba, avoiding any ambushes by them. However, the character's legs are still visible under the head, but they don't take notice. Made even more egregious by the fact that you can have many Goombas on your tail, but as soon as you put on the disguise they immediately stop. You'd think the Goombas would recognize those legs more easily, considering the countless times they've seen the bottom end of them.
Subverted in Super Robot Wars Alpha 3 and Super Robot Wars Original Generation 2, in which Elzam V. Branstein dons the identity of Ratsel Feinschmecker (German for "Mysterious Gourmet", a fitting time for an avid chef like Elzam) in order to fight alongside the heroes again. The "disguise" consists of nothing more than a pair of sunglasses and a slightly different style of clothing. The other heroes see right through it (except Arado, who isn't exactly the sharpest knife in the drawer, and Lefina, who is just too trusting when Ratsel tells her he isn't Elzam), but as officially having a former enemy pilot around might raise too many questions amongst the top brass, they play along with only the barest of efforts, often just substituting the name "Ratsel" when referring to Elzam, even if talking about something he did as Elzam.
The Elzam/Ratsel disguise is a Shout-Out to Mobile Suit Zeta Gundam, where Char Aznable, The Ace for Zeon, swaps out his full-face mask and helmet for a pair of sunglasses and goes by the name Quattro Bageena (it helps that he also falsified official records). At one point Ratsel even says "I am Ratsel Feinschmecker, no more, no less", pretty much word-for-word what Quattro said when Kamille accused him of being Char.
Considering the number of other enemy pilots that have joined the team (for example, Elzam's very own niece, Leona Garstein), the going theory is that he's doing it as a form of penance. Or something. Mostly people just humor him because he pretty much is the best pilot on the planet. And he owns a battleship with a drill on the front.
Subverted in Lunar 2: Eternal Blue Complete. One of the five heroes of the game is Leo, a Knight Templar who eventually does a Heel-Face Turn. At a point in the game before he joins you permanently, the goddess he serves throws your party in jail. A masked man named Mystere (who looks exactly like Leo-plus-domino-mask and uses the same attacks) frees the party, denies any connection, and chews the scenery a bit. Later, Mystere vanishes and Leo returns. No one's fooled, though they keep up the illusion for Leo's sake. Another character speculates that Mystere is how Leo rebels against the elements of his job as Knight Templar which offend his sense of justice.
In Mega Man 6 for the NES, a mysterious contest promoter known as Mr. X appears to be the villain of the piece...unfortunately he bears a staggering resemblance to the regular game Big Bad Dr. Wily, except he has sunglasses, a beard, and a dot on his forehead. Capcom had tried this in the last two games, with 4 having the Russian scientist Dr. Cossack as the villain until it is revealed Dr. Wily was simply blackmailing him with his daughter. 5 claimed Mega Man's brother Proto Man was the villain, but he was simply a robotic impostor called Dark Man built by - you guessed it - Dr. Wily. With this flimsy Mr. X disguise, Capcom were clearly not even trying anymore.
"You know who this is, right? Yeah, I didn't do any of the design."
The mysterious ??? guy who manages Proto Man's shop in 10 looks surprisingly similar to Auto with a Met helmet. With his cat sleeping on the counter. Yeah.
Team Fortress 2's Spy class (seen in picture at top) has a disguise ability that will make them indistinguishable from an opposite team member…to the opponents. To the Spy's teammates, he looks like a Spy with a cereal-box paper mask on (the mask shows his current disguise).
The original Team Fortress mod as well as Team Fortress Classic averted this trope, with the spy's disguise looking the same for all teams. Teammates had to aim their crosshairs at him to reveal his true identity.
The team's bases themselves, disguised as such things as granaries and shipping companies, sometimes qualify. The ones in Double Cross are said to "fool nobody", and 2fort's RED base, meant to be disguised as a farm, has a wooden cow. There are mooing sounds coming from somewhere, presumably a hidden tape recorder.
Lampshaded with the description of some of the maps, as they fool absolutely no one and sometimes the folks gather around to "watch the mercenaries fight over that spy base".
RED Soldier was contracted by Saxton Hale to disguise a old run down town as the Mann Co. International headquarters. This consist of crudely painting "Mann" over several signs, crossing out any letters after "Co", painting a "bomb hole" at the back of the town, and hastily building large, Hollywood-esque "MANN CO." letters over the main buildings. The Soldier even forgot to take his contract with him after halfway finishing the job. The result is the "Decoy" map used in Mann vs. Machine. The fact that legions of his robots are falling for this plan is what prompted Gray Mann to make the Engineer (although ironically the Engineer Bot can appear on this map, making it sort of Gameplay and Story Segregation and Hilarious in Hindsight).
RED Soldier also routinely sneaks into Gray Mann's base wearing a "robot" halloween costume◊ consisting of a cardboard box, two shoeboxes, and some dryer hoses. He doesn't even bother swapping his bright RED army fatigues for Grey ones. Hilariously, Gray himself doesn't notice the badly-disguised human either.
Subverted in Full Throttle. The villain hosts a demolition derby as a ploy to lure out and kill protagonists Ben and Maureen. Ben and Maureen enter the derby in disguises deliberately made to fool everyone except the villain, all as part of a Batman Gambit to fake their own deaths while keeping their true identities hidden from the derby's spectators. The villain even lampshades upon seeing them, "Who do they think they're fooling with those ludicrous disguises?"
Psychonauts' Journey to the Center of the Mind of a mad conspiracy theorist has robot-M.I.B. monotonously mimic different everyday roles of Suburbia, ranging from a housewife to an assassin, often using nothing more than one article of the occupation as a disguise. This also works for the main character, though, as merely holding a red sign functions as the perfect disguise of a road worker.
Their lines of idle dialogue are just as hilariously paper thin:
Road worker G-Man: My red sign helps me work on the road.
Assassin G-Man: I like to shoot people.
Sewer worker G-Man: Feces.
Possessing the items causes them to actually perceive you as a house wife/road worker/what have you rather than them taking for granted that the person who is holding the rolling pin is not someone remotely suspicious. Probably still qualifies but...
To a further degree, Raz can pass as the head of the mental asylum simply by using an award statue, an oil painting, and a strait jacket. The man working the elevator is nearly blind, but still....
The identity of the Cornstalker in Touch Detective 2 1/2 is supposed to be a big secret... but there is one character that has the same jawline, same hair, same basic build, very similar name, and most disconcerting of all, the same voice (or rather, squeaky tones). A visit to the portrait gallery after the very first episode is enough to figure out who he is.
Persona 4 expects even the player to think that all it takes for Naoto to be unmistakable for a boy is to put on a hat.
This is really only a problem in the English version, though. In Japanese, it's quite common for young boys to be voiced by women. In addition, Naoto's Japanese VA is Romi Paku - known for her portrayals of young men.
Rise also manages to convince a horde of curious bystanders that she is an old lady by... putting on an apron and tying her hair up.
In this instance, it works because they're looking for an idol, and she works in the back of the tofu store, keeping out of sight. When the police chase off all the bystanders and the main characters go to talk to her, her disguise lasts for about three seconds.
Atlus used this in the rerelease of Persona 2: Innocent Sin. For some reason, probably due to an international release and/or a new Japanese law, Adolf Hitler needed to be censored. So, all swatstikas were replaced with iron crosses and Hitler himself was given a trench coat and sunglasses while being called Fuhrer. Of course, anyone will know this is Hitler even though it turns out he's not really Hitler.
Celes at least picked up on it fairly quickly, but Edgar kept pushing Celes away in order to keep her (and Sabin if he was there too) from blowing his cover - he had a good reason to dress up.
Celes: Why the stupid farce? Edgar: I heard Figaro Castle got stuck after the Floating Continent fell. I wanted to help, but I didn't know where to look. Then I heard that those crooks had escaped from the jail. Celes: You intended to use them... Edgar: Bingo! I had to wait until they led me to their secret cave.
In Final Fantasy VII, Cloud and Co. disguise themselves as Shinra soldiers and sailors in order to get aboard a Shinra vessel. The humans pull off the disguise rather well, but it's hard to believe Red XIII, the not-terribly-anthropomorphic dog/wolf creature, managed to fool anyone...especially considering his tail was poking through the top of his pants and he was struggling to walk on two legs.
Bosco in the first season of the Sam & Max games. He even leaves his name tag on.
And after Max becomes the President of the U.S., Secret Serv ice-cream vans become ubiquitous.
In Ōkami, a game based partially on using a celestial, godly paintbrush along your quest, the main character, the wolf goddess Amaterasu, must infiltrate a nest of demons whose faces are covered with a paper decorated with a Japanese character. To fit in, a piece of paper is taped to Amaterasu's nose, and the player can draw whatever squiggles they like on it. None of the demons are any the wiser, making this disguise literally paper thin.
Lampshaded in that Issun, your Exposition Fairy, says that the mask probably won't work. He seems rather depressed that it actually does.
This happens no less than Three times in the sequel; they never catch on until the mask gets lost. Even more ridiculous, two of the three times has you infiltrating the exact same place and passing by the exact same demons, granted, you do re-paint the disguises all three times, but still...
Subverted in the Chocobo spinoffs of Final Fantasy. Mog wears an assortment of masks, disguising himself and giving himself a name like "Pop-Up Hero X", but thanks to his predictable use of "kupo", Chocobo eventually sees through him. In Choboco Tales, Shirma: "You're not fooling anyone except yourself."
This is an unusual example: the disguise works on the PCs, but the first-time player hasn't met Balthios yet and so has no idea who UH is even supposed to be!
Subverted in Fire Emblem: The Sacred Stones, in that both the protagonists disguise themselves as mercenaries. Also, their cover is never blown save for one random villager mentioning that one of them "carried himself in a royal manner".
However, it is double-subverted when one of your team members, reveals himself as long-lost, self-exiled prince Joshua. It's kept very well-concealed due to the fact that a fair amount of people from his country look similar (more so than most of the others), and also to the fact that He's a gambling addict who possesses no qualms about cheating on every game of chance he participates in and STILL manages to lose due to his famously low luck stats. The only hints we get of any noble nature whatsoever is his reluctance to kill pretty women, which can be attributed to his womanizing nature anyway.
For another Fire Emblem example, Devdan/Danved in 9 and 10 has a disguise that's beyond paper thin. His constant denial is absolutely the only evidence that the two are not the same.
In Blazing Sword, the player's army sneaks into Bern. The three lords don ragged brown cloaks without hoods. This is somewhat effective with Hector and Lyn, but Eliwood never bothers to take off his highly visible crown.
A much older example is Sirius, from Mystery of the Emblem. Even though pretty much everybody knows that he is really Camus beneath his Cool Mask, his true identity is never revealed (except if you count his Suspiciously Specific Denial when he snaps Nyna out of her Brainwashed and Crazy state in the Final Chapter as a very thinly-veiled confirmation).
Tallis in the new Mark of the Assassin DLC adventure for Dragon Age II gets her hands on the MacGuffin by putting an Orlesian guard's helmet on and letting the Duke hand it to her. This doesn't make much sense, due primarily to the fact that she's a female elf and thus a lot shorter than the normal guards, but also because she isn't wearing all that much clothing.
In Dragon Age: Origins, you can potentially escape from a prison simply by putting on a guard's armor, which doesn't conceal your face.
Whilst infiltrating the Arl of Denerim's Estate, you do so whilst dressed in stolen guard uniforms, which manages to fool most of the guards despite your party possibly consisting of Dwarves, Elves and Qunari. Lampshaded by Erlina, that Arl Howe has lowered recruiting standards and most of the guards are new.
In The World Ends with YouJoshua does this in his human form. He looks exactly like his Composer form only as a teenage boy, and only 2 people figure it out: Sho Minamimoto and low-level reaper Koki Kariya. It figures this is the same form he killed Neku with. Heck, he could have just put on a shirt that said "I am not the person who killed you." and that would have been better.
Lampshaded in Banjo-Tooie, when Banjo turns himself into a Stony in order to enter a kickball stadium (he still retains his backpack, his shorts, and the shape of his face). It seemed like he was foiled when the officer recognises him, but he is let in anyway as the participating players were running short.
Also, Liquid's disguise as Master Miller in MGS1 consisted of little more than putting his hair up, putting on some sunglasses, and changing his accent. He still had his distinctively dramatic way of speaking. It was pretty easy to see that it was Liquid at first glance. This was even more humorous upon the game's original release, as Master Miller had a very dark skin tone (not to mention black hair instead of blond hair) in Metal Gear 2: Solid Snake.
Of course it was retroactively subverted in the rerelease of Metal Gear 2: Solid Snake, and especially in Metal Gear Solid: Peace Walker, where it turns out that Master Miller really did look and sound like that.
Snake's "disguise" as Iroquois Pliskin in MGS2 has to count as well. It involves... wearing different clothes. That's it. Not to mention that the name he adopts is a reference to Escape from New York protagonist Snake Plisskin.
Metal Gear Solid 3: Snake Eater had something similar: EVA disguised herself as a KGB operative named Tatyana so she could get closer to Volgin and steal the Philosopher's Legacy. Her disguise basically consisted of... her wearing glasses and a slightly different hairstyle. Oh, and also a different outfit. Kojima even lampshades this in the director's commentary.
Similarly enough, Snake can easily fool guards when wearing the Scientist and Maintenance disguise (as long as he doesn't wear facepaint as well), despite keeping the bandana among other things, and even if the guards get suspicious, all he has to do to confirm he's a scientist is readjust his glasses. Now, if he encounters other scientists/maintenance crew members (depending on the disguise) face to face, that's a different story.
Inverted in the case of Snake meeting Volgin while disguised as Raikov. Despite being disguised so well that Zero claimed that even Raikov's own mother would not tell the difference, Volgin easily saw through the disguise (after pulling a Groin Attack on Snake twice). Hilariously double subverted during the final battle, where you can easily gain a free hit on Volgin if you wear the Raikov mask, without even changing into his officer uniform, and was missing the hat. To further add insult to injury, Volgin is fooled even though you put on the mask in front of him!
Subverted in his appearance in the Subspace Emissary story mode of Super Smash Bros.. Brawl, where Lucario easily saw through Snake's cardboard box trick (literally in this case, as he used his Aura sight to detect him).
Metal Gear Rising: Revengeance: Raiden's mariachi outfit. The minute he steps out of his car, two locals spot that he is a cyborg. They decide to keep their mouths shut and get out of there, however. Raiden even enters the sewers with Bladewolf right in front of them and says goodbye to them as he does it. While acting completely deadpan.
RuneScape uses this trope quite a few times where sometimes only changing one to three articles completely trick the NPC.
In "Eagle's Peak" quest, the player tricks other humans and eagles by disguising him/herself with a fake beak and fake wings.
In the "Branches of Darkmeyer" quest, the player fools the entire vampyre society into believing that the player is a vyrelord (one of the highest ranking vampyres), using only some quest-specific robes - despite the fact that vyrewatch and vyrelords have wings and can fly. The player cannot.
Also averted, in that even if you get a sex change, different skin color, different hair color and style, and a new basic wardrobe, most significant NPCs will still recognize you and call you by name - unless you're wearing one of the aforementioned disguises.
In Grand Theft Auto: Vice City, the cops will lose track of you if you go into your house in front of their very eyes, put on a "clean" version of the same outfit you were wearing when you walked inand walk out the front door, as long as you don't have more than two wanted stars.
Not to mention that in every game from GTA3 onward, you can drive almost any vehicle into a Pay-n-Spray in full view of the fuzz and be completely ignored when you drive out in the exact same vehicle. There are a few exceptions (buses, police cars, etc) which the Pay-n-Spray employees will refuse to touch, probably because they only come in the one color scheme.
Although amusingly, they will accept any taxi, even though they all have only one color scheme (usually yellow). This is especially prominent in the Vice City bank heist mission "The Job", where the mandatory getaway vehicle is a taxi, you have an automatic 4-Star wanted level (meaning SWAT teams), the Pay-n-Spray is literally down the street from the bank, and you don't even have to be out of the police's line of sight to use it.
Grand Theft Auto IV averts this trope while maintaining the game mechanic. You can escape the Police if you switch vehicles out of sight, though if they see you through the window, they'll recognize you and continue pursuit. Less realistically, you can still use the Pay-n-Spray to lose the cops, if they don't see you go in.
Subverted in Mother 3, where Lucas and his dog want to get into a nightclub, only to be informed by the bouncers that "No Dogs Allowed". The two slink away and seconds later, Lucas and his dog (now wearing human clothes and walking upright) walk up and try to enter. The guards aren't fooled, and even mention that Lucas was just here with his dog, and now conveniently walks up with a dude who looks like a dog. They only get in due to one of the staff members vouching for them.
Also played seriously when you walk in a Pig Mask base with masks for everyone except Lucas... who they mistake for their commander, of all people. That's because the Masked Man, the aforementioned commander, is actually your disappeared twin brother Claus reconstructed.
Played straight in the Chimera Lab, where the party only dons Pig Mask helmets, yet it's just as effective as when they wore full uniforms.
In Rayman: Raving Rabbids 2, Rayman's disguise manages to fool a Rabbid general holding a reference picture. Of course, the French titles of the original Raving Rabbids and this game translate as "Rayman vs. the Stupid Rabbits" and "Rayman vs. the Even Stupider Rabbits", respectively.
Of course, there was the immortal "It's just a big nosed bush" disguise in Rayman Revolution. Because big nosed bushes regularly spontaneously sprout on the way into your pirate stronghold. Sure.
In Assassin's Creed, all Altaďr needs to do to become a monk is to start praying. Guards will completely ignore him, including the multiple swords on his body, dozens of knives, metal gauntlets, assassin sash, etc.
In Etna Mode in the 2 remakes of Disgaea: Hour of Darkness, Enta manages to convince many people that Laharl is still alive by attaching a pair of antenna to a Prinnie that resembles Laharl's Expressive Hair. Vyers/Mid-Boss is one of the few people it does not fool. Given who he is, this makes sense.
Strong Bad's Homestar costume in Strong Bad's Cool Game for Attractive People Episode 1: Homestar Ruiner includes a makeshift head through which his eyes are clearly exposed. No one questions that fact. Nor do they question the fact that Strong Bad is several inches shorter than Homestar and has visible arms.
Averted in Dangeresque 3: The Criminal Projective, where Perducci's disguise is pulled off by using another actor.
In City of Heroes, Mender Silos, the leader of the Menders of Ouroboros, has the exact same hairstyle as Nemesis. To their credit, between that, the Significant Anagram, and the fact that most players would assume there's a connection between Ouroboros and Nemesis anyway, the developers know they're not fooling anyone.
In The Legend of Zelda: The Wind Waker, the traveling merchant Beedle apparently runs some sort of black market near one of the islands. His only disguise is a helmet. When you enter he immediately greets you as "Person who I have NEVER seen before"
Similarly, in Majora's Mask, the nighttime black market is run by the same person who runs the regular daytime market... in the same building. His "disguise" is a pair of sunglasses and taking off his wig.
Also in Majora's Mask, a few of the non-transformative masks (namely Don Gero's Mask, the Captain's Hat, and the Gibdo Mask), will make certain people and/or monsters believe you are someone or something else.
Kafei runs around Clock Town wearing nothing but a Keaton mask to hide his identity. In-universe it's justified because the Skull Kid turned him into a child and everyone who's searching for him is looking for an adult, but the player will likely not be fooled since they were given a mask modeled after him and his own mask fails to hide his distinctive hair. It's entirely possible to figure out who he is just by passing him on the street, but you can't call him out on it or tell anyone until you reach his Dramatic Unmask.
The Stone Mask, which looks like a weird stone face, apparently makes most people and monsters consider you to be as "inconspicuous as a stone". Interestingly, you can't see the NPC who gives it to you without using the Lens of Truth.
Not to mention every mask you can wear. Somehow people believe you are a female, a fishman or a large earth man because of it. No one seems to be able to notice you are 1/4 the size of any of them.
Link had been asleep for years and Zelda had grown up in that time, so that probably played a part.
Lampshaded in Lego Star Wars where a disguise is a moustache. Even on the women.
Stormtrooper disguises in Lego Star Wars 2. Just the helmet. This looks frankly ludicrous when it's Chewie wearing one, because it sits off kilter like a fez. It still fools everyone.
The really ironic part is that in freeform mode, you can play as a fully uniformed Stormtrooper, but all the other Stormtroopers will immediately know that you're not on their side.
Also in Lego Indiana Jones. It involves stealing a Nazi hat or a turban.
The mustache disguise is particularly amusing in the vehicle levels, where the spaceships wear mustaches...
In Lego Lord of the Rings, Eowyn briefly wears a false mustache. There's also Frodo's Elven Cloak and the Mithril Camouflage Tome, which disguise you as pieces of scenery. What's paper-thin about that is that you can move while disguised and it works. Nobody wonders why that crate is moving by itself.
In Arcana Heart, one of the characters, Kamui Tokonomiya, who is a thousand-something years old, and protector of Earth, is spotted by one of the other characters and it is immediately made known who she is. Her response? "But, my disguise was foolproof. I tied my hair back!". Add to the fact that she certainly STANDS OUT for carrying a katana everywhere...
Day Of The Tentacle: Laverne disguises herself as a tentacle with an outfit of the wrong color that leaves her head, arms and feet visible. None of the tentacles see through it, and a couple of them are attracted to her.
Xenosaga Episode III: The creator of T-elos, the more advanced version of KOS-MOS, is named "Roth Mantel". Roth Mantel translates to "Red Mantle". Guess who? Red Testament, aka Kevin. Granted, this is a bit stronger than most (since Roth only has a passing resemblance to his true self), but considering the thematic names of a lot of people in the series, and the fact that T-elos is remarkably similar to a prototype that had no plans that weren't encrypted ten ways from Sunday, Shion should have well picked up on it.
Either under this or the Wig, Dress, Accent, Wario Land Shake has a treasure called the 'Perfect Disguise'. Which is pretty much a pair of glasses and a false mustache, although apparently it works:
No one will ever know it's you!
In Donkey Kong Country, King K. Rool seems to make a habit of this. Subverted in that he fools no one (except, oddly, whoever it was who wrote his trophy description in Super Smash Bros.. Brawl), and there isn't even any real indication that he's trying to fool anyone. Apparently, he just likes dressing up in strange costumes and changing his title.
In World of Warcraft: Wrath of the Lich King, this trope is Played for Laughs. During the Death Knight (An unstoppable, undead killing machine) quest chain, you are required to intercept a messenger. You do this by disguising yourself as... a tree. Made of cardboard. Said messenger promptly remarks "What a strange tree. I must investigate". Shortly before the player leaps out and stabs him to death.
Later on in the Burning Steppes quest chain in Cataclysm, you're required to disguise yourself as a member of the Blackrock army using a mask that's the same model as the masks from Hallow's Eve (Which are just paper cut-outs). Most members of the army will fall for it, others will get suspicious requiring you to beat them to death with the cudgel one of the commanders gave you. Lampshaded by the person sending you to do the infiltration, who gives a dubious reaction on the order of "THIS is the brilliant disguise he's cooked up?! Okay, if he insists...." Which makes it even funnier when it does work.
Even more blatant when playing as a worgen. Yes, your naked chest is covered in fur. Yes, you have paws. And yes, you're running on all fours. But that paper mask says you're an ogre damnit!
Averted in Fallout 3, where it is impossible to disguise yourself. Your character is instantly recognizable, even dressed like this◊. Perhaps the wiki puts it best:
They are immediately hostile towards the PC, because he/she is American. (And that goes even for Asian-American characters wearing Chinese Army paraphernalia...)
If you walk up to the Outcast base in the DLC Operation Anchorage expansion wearing Outcast armor, you can fool them...for a few lines of dialog. It is a military organization, after all. On the other hand, if you walk up the Outcast base to trade high tech stuff with them while wearing their armor, you not only don't fool them, they will immediately take your armor without payment. (As they conclude that, at best, you stole it from a dead Outcast soldier, if you didn't kill them yourself.)
In Fallout 2 Goris, an intelligent talking Deathclaw companion for the player character would wear a brown robe to cover his appearance when not fighting. Absolutely nobody seems suspicious of the giant lumbering figure completely covered in brown cloth even though he's easily twice the size of any human.
Although it is ridiculously easy to fool the guards at the gates of Fallout 3's 'The Pitt'', just put on a slave outfit, they don't notice your wrist mounted computer or get suspicious about all your carried equipment.
In Fallout: New Vegas, putting on a faction's armor will automatically reset your reputation with them to Neutral so that if they're hostile to you they won't shoot you on sight so long as you have that on. This even works for things like Caesar's unique outfit, which can only be gained by either killing him or reverse-pickpocketing something with a better Damage Threshold. As usual, no one asks about your Pip-Boy, even if you're disguised as a member of the tech-hating Caesar's Legion. However, even putting on that disguise can make certain factions hostile to you, like the NCR while you wear a Legion uniform. Also, guards tend to see through the disguise and attack.
Then there's Nelly Cootalot, who can fool the aristocracy of Meeth into thinking she is Angelo Lightfoot, pilot extraordinaire...by stealing and using a fake moustache.
In the Medal of Honor series, someone always eventually sees through your disguise. For example, in Frontline, the guard at the entrance to the manor house says "You're not Friedrich! That uniform is wrong. You're an impostor!" Later, at the train station, you steal an officer's uniform, then the officer finds out and comes after you in his underwear. "Hey! That man stole my pants!"
In Soldier of Fortune's first Iraq level, you are provided with a disguise, but you soon run into a guard who asks you for identification (which you don't have), and your cover is blown.
In Golden Sun: Dark Dawn, two of the main antagonists show up in an early dungeon. One is a green-haired Blood Knight called Blados. The other is a bishonen guy with long blue hair, whom Kraden seems to know from thirty years ago, at the time of the first two games, in which one of the villains was a bishonen guy with long blue hair. But this can't be the same guy, he's wearing a mask!... that covers less than half his face.
In WWE SmackDown vs. Raw 2011, at one point in Rey Mysterio's storyline after angering the All-American American Jack Swagger you play as Evan Bourne against newcomer Todo Americano (which means All-American) who other than wearing a mask looks like Swagger, wears gear similar to Swagger, and has all the same mannerisms and moves.
Estelle in Tales of Vesperia is a princess, which she thinks is a secret. However, when her cover is "blown", she finds out that everyone in the party knew who she was...except Karol.
This trope returns to the Tales series in the PS3 version of Tales of Graces through a series of skits in which Richard takes on a superhero identity named "Masque de Baronia" to do good deeds for his friends. However, his 'costume' consists of little more than a turban and a piece of cloth covering his mouth, worn along with his normal attire. Of course, everyone instantly sees through it except for Asbel and Sophie.
Hubert unintentionally walks into this during his Disguised in Drag moment in the play in Fendel. It's lampshaded first, when an audience member points out that the evil queen looks just like Strahta's top Lieutentant. Then it's played straight when Hubert starts hamming it up and the man decides no respectable military officer would make such a spectacular fool of themselves.
In the SNES Shadowrun, two morgue workers become terrified of Jake after he rises from the slab they left him on (thinking he's a zombie), and refuse to have anything to do with him. Jake solves this problem by donning a pair of sunglasses, which stops them recognizing him.
Played straight in The Sims 3. If a sim who works as a private investigator goes on a stakeout, they will hold up a pair of shrub branches, and hide behind them, usually in plain sight. As seen here◊.
In Ragnarok Online, in order to get to the Rekenber Corporation's laboratory for various quests, you just have to wear a pair of geek glasses and a white mustache to get pass the guard guarding the laboratory, and the guard will allow you to pass even if you have a different hairstyle, clothing or even as a female.
The 1994 PC game Eagle Eye Mysteries in London has a mystery called "Case of Blood's Bold Bauble," where the protagonists have to get information from an obstructive hotel desk clerk. Your partner borrows another character's glasses and puts them on you, then pretends that you're the star of a new TV show and he/she is your agent. The kicker: the glasses is the only thing your (unseen by you) character's avatar wears in the way of a disguise, your partner doesn't even attempt to disguise him/herself, both of you are children (which means your partner shouldn't be old enough to be a TV actor's agent), the clerk will have presumably met you before (if you're playing the mysteries in the order they're presented), and the clerk still falls for it.
Lee Chaolan from Tekken enters the King of Iron Fist Tournament 4 under the disguise of Violet - which consists of dyeing his hair purple and wearing sunglasses. One wonders who he was trying to fool.
Occurs twice in MediEvil 2: In the Whitechapel level, Dan needs to find a suit and fake beard so he can gain access to a nightclub, and in the second sewer level, he regains the trust of the Mullock clan by wearing the same mask as the clan shaman (despite being at least twice as tall as him).
The SNK Gals FightersFighting Game has "Miss X", who is essentially the Badass Iori Yagami in a sailor uniform and a bandit's mask. Predictably, no one in the rest of the all-female cast falls for it, and all of them point it out immediately. Also falls under Creepy Crossdresser and Rule 63.
Recettear: An Item Shop's Tale features Recette and Tear utilizing a wooden-plank structure roughly crafted to be a tree prop, and labeled "totally a tree".
The disguise used by Freddy Pharkas: Frontier Pharmacist in the last act consists of a change of clothes, a neckerchief (which is actually worn around the neck), and a silver ear. Nobody realizes that the man with the silver ear is actually the one-eared pharmacist, up until the Big Bad captures him and removes the fake ear.
Masked Satan in Puyo Puyo TSU's Alternate Ending. The only change is a gold mask that only covered his eyes, yet he expects Arle to be unable to identify him despite having long green hair, horns, not altering his voice, and wearing the same blue clothing. Arle isn't fooled for one second. Even his name is a Paper-Thin Disguise, as when Arle asks "Aren't you just Satan?", Satan corrects her by saying he is Masked Satan, as if that makes him a completely different person.
In Peasant's Quest, Rather Dashing disguises himself as a bale of hay to sneak past the Jhonka and get its riches. When a strong gust of wind blows the hay away, revealing Rather Dashing, the Jhonka suddenly notices his presence, and asks him if he's seen his riches.
Batman: Vengeance has Bruce Wayne infiltrate the Funnibones warehouse in what has to be the worst gangster disguise in history. Notably, the Joker's thugs aren't fooled; neither are his fire-breathing jack-in-the-boxes.
Transformers: War for Cybertron has a "Disguise" ability for the Scientist class in multiplayer. All it does is change your color scheme to your faction opposite colors. Body-types are distinctive (especially so in the case of poor Shockwave), so it's easy for an experienced player to spot someone trying this and reduce them to a pile of scrap.
In Cave Story, you wear a Mimiga Mask to make other Mimigas talk to you when they wouldn't talk to you before.
Tse-tse Snaketail from Wizard101 does this multiple times using wooden noses and once some grass. Although he is an anthropomorphic zebra, manages to disguise himself as a lion, an elephant, and a rhino despite being nowhere near being the same size as any of the other species. Made worse by each time his fake names being just being a close variation of his real name like Tik-tik Snaketongue.
In The Night Of The Rabbit you find early on some lizards (poorly) masquerading as humans creep out everyone who sees them, in-universe. They're only able to start convincing people to take them seriously once the Big Bad's magic starts working.
In Normality, the resistance group comes to the stadium at the end of the game wearing fake beards and wigs (and the same clothes they always wear).
In Sheep, Dog 'n' Wolf, Ralph uses a couple throughout the game, all of which leave his face perfectly visible.
Octodad's entire disguise is sticking six tentacles through a three piece suit to act as arms and legs, use the two remaining ones to imitate a mustache, and causing plenty of property damage trying to walk and act humanlike. The only guy who catches on is completely nuts already, so they don't really listen to him.
Elite Beat Agents has "Mr. X", who is nothing more than Commander Khan wearing a cat mask. He doesn't even change the rest of his outfit, he just puts on a cat mask.
The Buzzy Beetles in Something Else disguise themselves as helpful ? Orbs, but that fails since they're always moving. Also, the ? Orbs are not used as exits.
Zigzagged with Furio Tigre in Phoenix Wright: Trials and Tribulations, who impersonates Phoenix in order to throw a trial he's involved in. When Phoenix finally meets him, he discovers that, other than similar hair styles and builds, the two neither look nor act anything alike (his fake attorney's badge is even made out of cardboard,) and wonders how the hell anyone could've mistaken them. However, when the prologue to the case plays, showing the end of the trial Furio sabotaged, he looks exactly like Phoenix (though this might be just to throw off the player.)