In a Silver AgeSuperman comic, actors are being auditioned to play Superman in an alien race's film. Since all humans look alike to the aliens, a severely overweight, middle-aged actor gets the role, because he heroically saves the day. The aliens can't distinguish him from Superman physically, but his bravery was enough to get him cast.
In one of the original Justice Society of America comics, Johnny Thunder puts on a cap and gown and an obviously fake mustache (that make him look like... Conan O'Brien in a cap and gown with a big mustache, for some reason) to fool some criminals, who are more puzzled than fooled.
Green Arrow, despite having facial hair that can most kindly be described as 'extremely distinctive' used to hide his identity as Oliver Queen behind a mask that was little more than a pair of tiny, diamond-shaped pieces of cloth with eyeholes cut out. Finally subverted in Longbow Hunters, when Shado openly expressed surprise that it was supposed to be a secret. Oliver Queen was also the mayor of his city. So literally the Mayor with very distinct facial hair was fighting crime in a lazy disguise and it worked. Also subverted in Mia Dearden's origin story.
Mia: Oh, please! I'm not a total idiot! That little mask you wear doesn't exactly Batman your face. And the beard's a dead giveaway, too.
Pointed out by Linkara in The Stinger to his review of Identity Crisis, expressing disgust at Green Arrow's claim that they had to "work at" keeping their secret identities (through mindwipes).
Lampshaded in the New 52Justice League of America series. Green Arrow wakes up in a hospital bed and finds he's still wearing his mask, and is told by Steve Trevor that they left it on to protect his identity. Ollie bemusedly points out that the mask does very little to actually protect his identity if he's not wearing his hooded costume.
In The Tick comic, the story "Night of A Million Zillion Ninja" features scores of evil ninja standing around a house that they are staking out, each one holding a single twig. To passers-by they state, "We are a hedge. Please move along." The homeowner is entirely fooled, though he doesn't remember planting a hedge in the first place.
The SupermanExpy, Caped Wonder took Clark KentingUp to Eleven. He wore glasses, which fooled everyone except the Idiot Hero. A fight between the two heroes occurs and the glasses are broken. The Caped Wonder does the "nerd glasses" hand signals in order to disguise himself when a co-worker shows up.
In PS238, it is suspected that this may be Tyler Marlocke's only super power. Keeping your secret identity in this world full of supers is described as being "as hard as keeping your email from spammers." Yet no one recognises him as Moon Shadow. Not his classmates, not his parents. He goes so far as to leave the room as Tyler and come back as Moon Shadow and nobody figures it out. He's very disturbed by this.
Tyler: That shouldn't have worked!
However, his non-superpowered best friend is unaffected by this, to the point of wondering why Tyler is wearing a silly costume when he first meets Moon Shadow.
Taken Up to Eleven by Toby, a clone of Tyler that has superpowers. Due to how he was made, he has all of Tyler's memories... except, somehow, the ones related to Tyler being Moon Shadow.
Gaul: Halt! Who Goes there? Caesar: A barrel you dolt! Gaul: Oh, a barrel.
In "Asterix in Switzerland", in order to sneak past the Romans, Petitsuix disguises Asterix and Obelix with a bow and arrows.
In all fairness, the Romans in Geneva did not know Asterix and Obelix by sight, so all the disguise was supposed to achieve was to make them appear like Helvetii, not foreigners.
In Asterix and Cleopatra, Obelix attempts to disguise himself as an Egyptian worker in order to get some magic potion by wearing an Egyptian headgear. Getafix is not fooled, to Obelix's utter bafflement.
Clark Kenting. Explanations vary for how the disguise is more extensive than the comics page shows, but it's still iconically remembered as a pair of glasses.
Several of the Young Avengers, as they largely didn't wear masks of any kind. Cassie and Eli wore a Domino Mask each, but also modelled themselves after her father and his grandfather respectfully (Scott Lang, Ant-Man II, and Isiah Bradley, the prototype Captain America), otherwise the rest of the group at best wore goggles and/or Cool Shades (Tommy and Kate), or simply nothing to hide their faces (Billy).
Subverted in Don Rosa's story "The Last Lord of El Dorado", in which Flintheart Glomgold follows Scrooge and his nephews with a series of incredibly obvious disguises (including a female waitress and a nun - Glomgold's beard made things even more obvious). When he reveals himself, however, Scrooge mocks him and tells him that he'd known all along it was him. (Donald was fooled, though.)
Hey, he's still better at disguises than the Beagle Boys. At least he doesn't wear a black mask while he's trying to disguise himself as a waitress. They pulled it off well a number of times. A group of Beagles wearing hollowed out Robots passed undetected for robot workers, and a latex mask was all it took for each of them to look like a grizzled old lighthouse keeper. And those are examples of when they were really making an effort. Their favourite disguise is a false beard.
Magica De Spell tends to use magic for her disguises, but unless copying someone who looks nothing like her, she tends to end up looking like herself in different clothing and a wig. Add to this the fact that even allowing loads of Negative Continuity, she must have pulled off the same trick almost as many times as the Beagle Boys. You'd think Scrooge would learn to beware of groups of identical stout guys with beards and sunglasses or duck women with green eyelids making him offers that are too good to be true. But since most writers in the comics aren't anywhere near Don Rosa's level, one of their favourite moves for getting the story going is to hand Scrooge the Idiot Ball at the beginning, to this effect or some other. (At least Magica often uses various kinds of hypnotic perfumes or other substances to make Scrooge a bit more suggestible, though they usually aren't effective enough to actually make him give up money, let alone his First Dime.)
Justified in The Maxx. The Isz have a latent psychic ability that convinces people looking at them that they're actually human whenever they put on a disguise, despite the fact that they're little dark blue Plant Aliens with lots of teeth. Note that this apparently only works on people who don't know they're doing it.
Super Goof is just Goofy in long underwear, but only his nephew Gilbert can recognise him.
On House of Mouse, when everyone tries to figure out who Super Goof is, they come to the conclusion that it's Dumbo.
For a while, Captain America disguised himself as a hero known as The Captain. The costume looked identical to his normal Captain America costume except for darker colors and a slightly different chest-insignia. He even threw a shield around which was also had a slight color-change. Here is a cover depicting both costumes.◊ This costume somehow fooled everyone, including his allies in The Avengers. The costume would later be worn by the USAgent.
Deadpool tries disguising himself at an A.I.M soldier in order for him and Captain America to get Wolverine's DNA and prevent them from cloning him. His disguise is nothing but a yellow trash bag, but it still sort of works—the soldier he talks to naturally notices that it's a trash bag and not a real A.I.M. mask, but assumes that the person wearing it is a real A.I.M. Soldier who's wearing it as a joke. (After all, what's more likely? That somebody risking his life to infiltrate A.I.M. would actually use a trash bag as a disguise, or that a workmate would goof around?
Deadpool: S'up? You got Wolverine's DNA here?
A.I.M Soldier: Is that a trash bag on your head? Karl? Quit goofing around, man.
An early Paperinik story has every belittled husband in Duckburg dressing up as Paperinik and playing mean pranks on their Paperinik-worshipping wives to ruin his reputation. Despite the fact that none of them look remotely like him (most of them aren't even ducks!), it works perfectly — at least until the real Paperinik takes action and exposes them.
Vathek: Dou you plan to disguise me as a bird or a stone?
Wolverine's disguise when roving Madripoor when he and the other X-Men were thought dead consisted of an eyepatch and refraining from using his claws. An old friend eventually informed the 5'3" tall extremely hairy man with the odd hairstyle that the only reason none of those who knew him called him on it was fear of getting gutted.
Jubilee also remarked once how lame a disguise it was. (Seeing how she was one of a select few people who he didn't mind sarcastic comments from.)
Subverted slightly in the Sensational She-Hulk graphic novel. After being taken hostage by S.H.I.E.L.D., the heroine manages to escape from her cell by reverting to human form and slipping through the bars. However, her attempt to pass through the Helicarrier incognito as Jennifer isn't very successful; no one actually recognizes her, but when someone notices she's barefoot, it's sort of suspicious. (Of coure, it's doubtful she thought it would work, but it's not like there were any better options.)
In issue #3 of My Little Pony: Friendship is Magic (IDW), Pinkie's plan for avoiding themselves getting mixed up with disguised Changelings is to wear costumes of themselves so that they can recognize each other.
Iznogoud: Iznogoud's idea of disguising himself as a pumpkin seller is to carry a pumpkin around. And it works, too. It works so well his own guards won't let him back into the palace until he drops the pumpkin!
In The Movement, Virtue goes to see Captain Meers of the police without wearing the small mask that she uses when she fights crime.
Atomic Robo's archnemesis, Dr Dinosaur, is capable of disguising himself as virtually anything by donning an appropriate hat and shirt. For the uninitiated, Dr Dinosaur is a dromaeosaurid. He is a rich orange-brown colour, with scales, eyes mounted on the side of his head, and an enormous mouth full of needle-sharp teeth. This is akin to disguising yourself as a wolf by putting on a jumper made from grey wool. It usually works perfectly up until Robo or another major character sees him, at which point he tends to be outed.
In Big Trouble in Little China, when Jack takes Pete to Chinatown to find out if his friends can break the black magic bond between them, Jack disguises him with a baseball cap, sunglasses, spiked dog collar, and a t-shirt, none of which in any way hides the fact that Pete is a gigantic, furry hell-beast.
A recurring element of Batman lore is Matches Malone, a cover identity Batman assumes occasionally. It consists of Bruce Wayne with a fake mustache, a plaid suit, and a match in his teeth. It's generally proven effective - sometimes lampshaded, sometimes not.
In older Batman comics, The Joker and the Penguin would sometimes go out in public "disguised" by nothing but a pair of Lennon Specs. It's a toss-up as to whether it's this trope or everyone was just too shit-scared to call the cops anyways.
The Joker also has this problem with his aliases. One of his favourites being "Joseph Kerr".
Deathstroke's daughter Rose Wilson (aka Ravager) is an Asian girl with silver hair, a look that isn't exactly common. Lampshaded when Robin points out the absurdity of Rose having a costumed identity despite making no effort to disguise her distinctive hair.
Robin: What's the mask for, by the way? I mean, who's she fooling? How many hot chicks with silver hair are walking around? "Gee...I wonder who that could be!"
The comic book version of Howard Zinn´s book A People´s history of American Empire has a FBI agent spying on activist Dan Berrigan in 1970, wearing Groucho Glasses and a wig.
Many old-school comics, even up until the 90s, had superheroes disguising themselves by... wearing a trenchcoat and hat over their brightly coloured costumes, leading to scenes such as Captain America managing to infiltrate a hospital in such a disguise over his usual outfit, which includes a bright blue head-covering cowl.
Gets even more surreal with Fantastic Four member The Thing, who in the past would try to disguise his rock-like features with a hat, trenchcoat and sunglasses. Ben is six foot and change tall, roughly three feet wide, and has skin that requires careful analysis to distinguish from segmented orange stone. Even in New York, that stands out. These days, Ben doesn't really bother.
The Golden Age Flash wore no mask at all. He simply vibrated to keep his features blurry. How it worked when he'd get knocked out is anybody's guess.
Green Lantern: Hal Jordan's disguise consists of a tiny domino mask. Combine that with Hal's usual Idiot Hero tendencies, and it's amazing he has a secret identity at all. His buddy the Flash even commented on it at the beginning of Blackest Night.
Monty The Dinosaur: Before he met Sophie, the closest Monty ever got to a human was one time wherein he wore a fake mustache and nothing else. Said fake mustache tickled his nose, causing him to sneeze it off and blow his cover.
Wonder Woman (1942): Queen Clea thought she could trick Steve Trevor by wearing a trench coat and holding the sleeve up over her mouth. Without removing her very distinctive headgear. Steve was not fooled, but pretended to be in order to get her to drop her guard so he could arrest her.