In one early issue of Grant Morrison's Animal Man, Buddy's getting his ass handed to him by a much stronger enemy, and tries to use stealth to escape him instead of fighting back. To do it, he uses his powers to absorb a nearby chameleon's color-changing abilities, hoping that he can use them to blend with a rock face and camouflage himself. He forgets that he's wearing a brightly colored full-body spandex suit that doesn't change color along with his skin. Naturally, the ruse doesn't go so well.
Aquaman's lifetime in the sea leads to increased strength, agility, and resilience on land that would help him to survive and move easily in the ocean depths. How much of an increase ranges from "tough enough to give most B-listers a real work-out" to "evenly matched with a Kryptonian or Themiscyran on dry land, probably got an edge on them with his Home Field Advantage", Depending on the Writer and continuity.
Technically, Aquaman always had superstrength and durability, at least in his first Golden Age appearances, that were forgotten during the Superfriends era. On the splash page of his very first appearance, More Fun Comics #73, he's shown deflecting an artillery shell with his hand.
Grant Morrison also gave him the ability to essentially induce seizures by telepathically touching the part of the brain that humans share with fish. It's a shame that he doesn't do that more often.
During the "Justice League Detroit" days, he was shown being able to influence people's actions through the same "fish portion of the brain" excuse. How little sense this makes is the least part of why many people deny the JLD ever happened.
Geoff Johns explained that the second Aqualad possesses superhuman vision as a result of his eyes being designed to see even while at the bottom of the ocean, where there is obviously little to no sunlight.
In Aquaman: Rebirth, Mera complains about fielding endless questions how she keeps her hair so full and lustrous despite spending so much time in salt water. Although some artists will draw Atlanteans with their hair looking realistically wet and flattened down when they surface, or with long hair floating around their head when submerged, they are more often drawn with their hair looking perfect on land or underwater. This must mean that Atlanteans have natural oils which protect their hair from undersea conditions.
And people have thought of all kinds of creative ways for him to use his power to "Command the creatures of the deep!", such as the page picture for Heart Is an Awesome Power. Canon hasn't quite gone to that extreme as yet, but he once decisively ended a fight with Namor the Sub-Mariner with the help of a passing orca.
Birds of Prey: The young teleporter Misfit astounds Barbara Gordon because she defies the usual Teleportation with Drawbacks. She can "bounce" (her term for it) anywhere, no matter how far away, without even having to visit the place beforehand. She instinctively avoids teleporting into objects. And she can "bounce" any number of times without exhausting herself. She actually heals herself each time she does this, and recovered from a gunshot wound this way in her debut. The only limitation of her ability is that she can't take other living things along for the ride — they die when they reappear. Misfit discovered this when she tried to bounce herself, her mother, and her little brother out of their burning home and accidentally killed them this way. A later storyline revealed that her powers are magical in nature, explaining this somewhat.
Another character originating in Birds of Prey is Black Alice, Misfit's cousin, who can steal anyone's magic powers and use them as her own. Unfortunately, she doesn't get their control, as she discovered when she tried to use magic to fix her father's near-sightedness — and ended up giving him cancer instead.
The Button: Eobard Thawne/Professor Zoom breaks into the Batcave and beats Batman up. When Batman tries to fight back, Thawne turns himself intangible and gloats that Batman can't hurt him. He is proven wrong when Batman stabs him in the foot. Batman points out his feet would have to be solid or else he would sink into the ground.
The Flash's powers are an all-inclusive package called the Speed Force, but parts of it come and go for the purposes of a given story. For example, his seeming ability to slow down his required super-perception has been pointed out a few times. In the Justice League episode "Only a Dream", for instance, the villain Doctor Destiny tormented superheroes with various nightmares; the Flash dreamt that he was unable to slow down, and perceived everything around him as motionless. The idea of a Flash unable to slow down his perception was also eloquently expanded upon by Jim's Big Ego in this song.
Flash doesn't always have this ability. In one comic he spent a subjective week watching a movie with his wife. This would be really painful, given that persistence of vision wouldn't work, and so you wouldn't even be able to perceive the motion in the movie properly. It would be like watching a slideshow of someone's vacation pictures. Or rather like watching a procession of phosphorous dots or pixels cover the screen one at a time, possibly building up to a coherent picture at the end. For every single frame of the movie. At least one comic has explained this as being subconscious. When he is bored he tends to zone out and activate his speed without meaning to. This means that a conversation with his father in law, or a trip to the opera, can take forever.
Right after Crisis on Infinite Earths, Wally West had to eat huge amounts of food to fuel his powers. Later, it was revealed that the semi-mystical Speed Force provided both the energy and the friction shield.
Early in volume 2 of The Flash, Wally discovered a new trick with the aura that protects him from air friction. He can consciously remove it from objects he's carrying, thus exposing them to extreme heat. (This was of limited use against the robotic Kilg%re, but still.) He hasn't used this much since, but it's a fine, rare example of a weaponizedRequired Secondary Power.
Super speedster Bart Allen (first Impulse, then Kid Flash, then regular Flash until his untimely death) was once shot in the kneecap by Deathstroke. At the hospital the doctors discovered, to their horror, that his hyper-accelerated metabolism had already begun to knit the broken bones back together and they would have to break them again so they could be set properly. They also couldn't use any anesthetic because his superfast metabolism would purge it out of his bloodstream too quickly.
Bart also discovers that he can't have a tattoo because of this. After impulsively getting a Green Lantern logo tattoo (because who would suspect a guy with Green Lantern's logo tattooed on him being Kid Flash?) he finds that it quickly fades away, as if decades of epidermal rejuvenation were taking place in a few seconds. One wonders why he doesn't leave piles of skin cells everywhere he goes.
The Elseworlds story Batman: Holy Terror had a villain who'd worked out how to switch off Barry's friction aura. He does this when the Flash is moving at full speed. (Further Fridge Logic, however, suggests this should result in Barry's flaming corpse slamming into the guy at hundreds of miles per hour.)
Explicitly acknowledged in Justice League 3000, where the new Flash lacks the original's connection to the Speed Force, and thus becomes violently ill whenever he tries to utilize his speed abilities. Cadmus ends up equipping him with artificial force fields to keep him from hurling whenever he tries to move quickly.
The Flash's tie-in to Armageddon 2001 shows a potential future (averted by the end of the annual) where Wally West has a son named David who inherited his speed, but not his protective aura. The boy seriously injures himself saving a young girl from a speeding truck. It's hinted in the Justice League America tie-in that heroine Fire had an even worse tragedy when her offspring didn't inherit her protection from her own flames.
In the first issue of H-E-R-O, a man uses the HERO Dial to turn into Afterburner, a Flying Brick who, as it turns out, is not nearly as Nigh-Invulnerable as he looks; the guy ends up nearly killing himself saving a little kid from a drunk driver in a semi.
Citizen Steel is super-strong and invulnerable to harm but has an extremely stunted sense of touch as a side-effect of his powers. It's to the point that he gets really happy when he faces a foe strong enough to cause him pain, because it's a feeling. Another problem he suffers is holding back; a metal suit has to be cast around him to bring him down to a level of super-strength where he can actually function without destroying everything.
In issue #75 of JSA, Atom Smasher explicitly mentions breaking and regrowing his bones and muscles as he grows. While it has never been done, this would theoretically allow him to heal bone and muscle damage by simply shifting height again. He also has a specific height (around 50 feet) wherein his powers start to malfunction and the Square-Cube Law starts paying attention to him again.
Subverted in a story in which Superman encounters a new superhero while rescuing some firemen from a collapsing building. The newbie has super strength and is able to hold up the falling ceiling long enough for Superman to evacuate the firemen. Unfortunately, he discovers that he does not possess invulnerability and is killed when a gas main blows up in his face.
In a Bad Future issue of JLA (1997), Connor Hawke and The Atom were able to penetrate Darkseid's supposedly impenetrable force field by exploiting the fact that light waves could pass through it. The Atom reasoned that if the field actually shut out light, Darkseid would be blind.
Brainiac Five has a force field belt that (before Crisis on Infinite Earths, at least) was explicitly noted to have the ability to automatically generate breathable air whenever creating a closed shield. Even before he invented the transuits, it was stated that he didn't need a conventional space suit for this reason.
Night Girl (super strength and durability, but only in the dark) and Shadow Lass (generate and control darkness) both have the secondary ability to see in the dark.
Fellow Legion member Ultra Boy is a twist on the standard Flying Brick powerset — he has Kryptonian-level abilities (including equivalents of heat and x-ray vision), but he can only use them one at a time. This means that he's often seen using Superman-level strength, whilst still being as fragile as a normal human (well, Rimborian, but same diff), meaning that the slightest movement should have ripped him apart, not to mention that every time he tried to lift something heavy he should have been completely crushed, and punching anyone or anything particularly durable should have shattered every bone in his arm.
This was explicitly acknowledged several times: for instance, in the Silver Age he was technically fast enough to travel through time under his own power (like Superman could), but he would have been totally atomised by friction if he ever tried to move at that kind of speed.
Bouncing Boy is a rare case where the required secondary powers actually became more prominent than the primary one. Because of the impressive ricocheting moves he pulls off, the writers reasoned he must have an innate knowledge of geometry and mathematics, so he became one of the Legion's main science guys and rarely used his primary power. Thankfully. And he's a great billiards player — he knocks three balls into the nets with one strike!
Durlans, a shape-shifting species which Chameleon Boy is a member of, were eventually revealed to have an extra sense that allows them to scan all the cellular and anatomic details of a new being they encounter, as well as perfect memory for same. For which their antennae are the sensory organs.
"Those Emerald Eyes Are Shining": Played with when Supergirl is trying to move a planet. She has the strength, but attempting to do so just ends up digging a hole through the planet because she can't move it as a single object by touching a small part of it. However, the "solution" used is to have her bounce into the planet, which really should fail for the same reason.
Red Robin: Wanderer, the leader of the Council of Spiders group that tries to kill Tim Drake, is immune to her own poison.
It's arguable that most flying heroes possess an innate sense of direction that seems to keep them on course no matter how far they are flying. Superman is explainable via his vision powers, but most don't have that. However, the Will Payton version of Starman would actually follow highways and later carried a map when he got a suit with pockets.
In one of the Superman annuals (as part of the Legends of the Dead Earth line), there was a team of heroes, each of which having one of Superman's powers, but the powers were either stuck "on" or coupled with potentially hazardous side effects, even when those were powers granted by a "supersuit" rather than bio-modification. The speedster's suit had to keep her blood sugar levels up and the super-breath guy's collar worked both ways, so he could have ruptured his lungs if he breathed in too suddenly. Of the bio-modified heroes the super-strong one couldn't even feed himself because he would crush the spoon and the food, the X-ray eyes hero saw everything in X-ray eyes and had to wear special lead glasses, the flier had to be tethered to something because if he wasn't deliberately moving towards something he could drift away, the heat-vision guy had to discharge the energy from his eyes every so often to prevent a fatal buildup, and the invulnerable one had no sense of touch.
After the 1986 revamp, Superman was assumed to have some version of touch-based telekinesis, as there's no other explanation for why he can lift up giant objects without the part that he's holding simply overbalancing and ripping free, or how he can catch falling objects (and people!) without doing them harm from the sudden stop. On at least one occasion Superman did comment that things felt different when he was carrying them while flying than they did if he lifted something similar when not flying.
This was tacitly acknowledged to be true when he was cloned, resulting in Superboy. Superboy's only power was tactile telekinesis, which he used to "fake" stuff like flight, invulnerability, and super-strength, until eventually his Kryptonian genetics kicked in and he got them for real.
Superman and Supergirl's heat vision started out as a seeming Required Secondary Power of their X-ray vision. It was originally assumed that power worked by projecting X-rays and that they could focus this to generate heat. Now it seems that they are separate powers.
In "Supergirl's Big Brother", a crook tries to make a super-pill to give himself Kryptonian powers; however, he uses the wrong mix of chemicals, and his invulnerability wears off when he is swimming through the ocean, leaving his body unable to bear the water pressure.
The miniseries Trinity (2008) explicitly acknowledges the physical difficulties Superman should have when moving objects with a large momentum — e.g., when a runaway train hurtles towards a turn, he first tries to force it into the turn by pulling it, and only succeeds in ripping the wall off; he needs to deflect a nuclear missile fired at a satellite, he can't hope to deflect the whole thing in time, so he cuts off the warhead and deflects it by itself, and needs to grab onto an asteroid to stop inertia carrying him past the asteroid belt; he can't simply pull two drone planes hurtling towards a skyscraper out of the air, but he can take advantage of the fact their wing structures make them steerable and force them on a collision course with each other and send them crashing into the sea.
In Kryptonite Nevermore, a villain removes Superman's powers one at a time. At one point, he is about to land, but loses his strength at that very moment, and as a result plows into the ground (he was still invulnerable). He points out that even though he still has the ability to fly, he needs the super-strength to coordinate his flying and landing.
According to some accounts, Kryptonians have a forcefield that extends a few millimeters past their skins. Which explains why Superman, Supergirl, Superboy, Power Girl... costumes stay intact while their capes get ripped. But not why the cape is fine at superspeed. Depending on the version, the cape is the blanket Superman was sent to Earth with, meaning it's more or less indestructible. In some versions, the entire costume is made from it. Also would explain why they crack the ground in a circular fashion when they're holding something heavy up or landing hard ,under their own will, instead of sinking directly into the ground or cracking in a more logical fashion.
One comic from Smallville: Season 11 explains that when Superman makes himself immovable, it's not only his invulnerability: he's also using the same control over his personal gravity that he uses to fly.
Even Kryptonite has a Required Secondary Power: it causes Kryptonians to be severely weakened in its vicinity. This prevents them from simply hurling the rock away before they take too much damage.
In Two for the Death of One: Action Comics #535-541, Lord Satanus and his sister Blaze are playing magical tug of war with Superman — and accidentally split him into two people, each with only some of Superman's powers. One has flight and super strength. The other has invulnerability. Their magic spell would flood him with enough magical energy to kill him, so they need the invulnerability to process it. They didn't need the other one, so they leave him in the present and go back into the past. Now vulnerable, this superman can't fly supersonic or lift anything as heavy as a car without extreme pain.
Superman's hearing must have some component of this during its more powerful examples. The 1986 revamp explicitly omitted the more extreme examples and he reminded Jimmy that the signal watch wouldn't work if he were too far away. It was later reverted to Silver Age levels where he could "hear" across the vacuum of space (including one issue when he was in another solar system 25 light years from Earth) and could "hear" Lois' heartbeat halfway around the world. Some form of telepathy might explain it.
Silver Banshee has Super-Scream abilities. She is immune to her own scream, as well as sonic attacks from others, like Black Canary's Canary Cry.
In a Post-Crisis story, Jimmy Olsengains stretching superpowers much like Elongated or Plastic Man. The problem is he lacks any ability to control said stretching nor the required secondary power to deaden the pain that such stretching would naturally cause like the aforementioned superheroes do. He's nearly driven insane from the ever-increasing pain as a result during the ordeal.
In The Vigil, Dodge's powers allow her to move faster than the eye can see, but Dr. Sankaran had to reinforce her skeletal structure to deal with the resulting strain.
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