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.
Alternate Company EquivalentQuicksilver explicitly doesn't have this: while he can slow down his perception as he speeds up, his default is still faster than human normal. It's described as the reason that he's so cranky: everyone else is moving at a snail's pace.
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.
In an "Elseworlds" story set in the future, Flash's son inherited his speed, but not his friction resistance, with the tragic potential being explored.
Another Elseworlds 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.
In one of the Superman annuals (as part of the "Legends of the Dead Earth" motif), 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's heat vision started out as a seeming Required Secondary Power of his X-ray vision. It was originally assumed that his X-ray vision worked by projecting X-rays and that he could focus this to generate heat. Now it seems that they are separate powers and his X-ray vision works by attuning his eyes to perceive X-rays (this in turn was extended to allow him to see an increasingly broad range of the electromagnetic spectrum).
The 2003 miniseries "Trinity" explicitly acknowledged the physical difficulties Superman should have when moving objects with a large momentum, e.g. when a runaway train hurtles owards 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.
John Byrne, who revamped Superman, had previously used the explanation for Gladiator over at Marvel, who was a Superman-ersatz from the Imperial Guard, themselves an Alternate Company Equivalent of the Legion of Super-Heroes. In Gladiator's case his power level is explicitly affected by his state of mind— loss of confidence makes him physically weaker.
This was parodied in Wild Cards by Golden Boy, who when rounding up Nazi war criminals attempted to do things like stop cars, bend tank turrets into knots or lift a tank up by the turret, but invariably the gun barrel would rip off or he wouldn't have the leverage, and cars just sent him flying. Eventually, he gave up and resumed just knocking them over or tearing them apart from below.
The "using-telekinesis-to-fake-strength" power is common enough in the Whateley Universe to have a name, "TK Brick". Hank (aka Lancer), one of the main characters, is one.
In one Silver Age story, 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, Supes has a forcefield that extends a few milimeters past his skin. Which explains why his costume stays intact while his cape gets 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.
One comic 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.
In 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.
Sometimes, the Required Secondary Powers pop up when the writer wants to find some way for a superhero to make up for their somewhat less satisfying powers. Aquaman's lifetime in the sea leads to an increased strength, agility, and resilience on land that would help him to survive and move easily in the ocean depths.
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.
A villain from Static had the ability to absorb matter directly into his body, which resulted in him becoming so dense as to be impervious to all weaponry and super strong... but he wasn't quite strong enough to move well with his weight. He was eventually defeated by forcing him to absorb so much matter he become too heavy to move... so heavy, in fact, they had to use the NASA Crawler to haul him to jail!
Another was Rubberband Man, who once turned into a vacuum cleaner to avoid being caught by Static's sister. When Static's sister tried to wheel him out of the room, she found it rather difficult because A. he still weighed the same, and B., as he put it, "Wheels are hard."
Durlans, a shape-shifting species in the DCU, 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.
Strangely both averted and used in Legion of Super-Heroes V2. 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.
In a Bad Future issue of Grant Morrison's JLA, Connor Hawke and The Atom were able to penetrate Darkseid's supposedly unbreakable 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.
The young teleporter Misfit introduced in Birds of Prey astounds Oracle because she effortlessly avoids nearly every complication associated with teleportation. 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.
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 JLA story where 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.
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) who both had the secondary ability to see in the dark.
Fellow Legion member Ultra Boy was a twist on the standard Flying Brick powerset- he had Kryptonian level abilities (including equivalents of heat and x-ray vision), but he could only use them one at a time. This meant he would often be seen using Superman-level strength, whilst still being as fragile as a normal human (Rimborian actually, but same diff), meaning that the slightest movement should have ripped him apart, not to mention that every time he tried to punch something or lift something heavy he should have been completely crushed.
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.
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.
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.
Wanderer, the leader of the Council of Spiders group that tried to kill Red Robin, is immune to her own poison.
Implicitly acknowledged with the Marvel Comics "Decimation" arc, where several mutants keep their primary powers but lose the secondaries. Mutants with fire abilities are no longer immune to their own flames and incinerate themselves, a dragon-like mutant falls out of the sky because his mass can't stay airborne under normal physics even with the wings, a fishlike mutant drowns because his gills can't extract enough oxygen from the water to support a human body, and so forth.
The miniseries Galacta: Daughter Of Galactus suggests that the mutant gene does not actually confer superpowers on people but, as a result of extensive engineering by The Celestials, alters reality to make mutant powers possible, thereby making every mutant a low-level, unconscious reality warper, Handwaving every impossible thing that mutants do.
In a Spider-Man comic where Doctor Strange's mansion was destroyed, there were these floating masks (if memory serves, they had something to do with Cyttorak), who could "wear" human faces and fire laser beams while doing so. Too bad they couldn't sustain the bodies...
Chris Claremont usually averted this, giving the X-Men their Required Secondary Powers explicitly and having some of them learn to use them on their own. However, he wrote one of the junior team, Sunspot, as super-strong but not invulnerable, which led to a letters-page discussion about why the character didn't break bones while lifting things.
Also, though it may not have had anything to do with Claremont's work, some of Wolverine's secondary "powers" have been indicated: When Rogue got a full taste of his Super Senses she was overwhelmed by the sensory input (and in intense pain, as the tactile sense was in overload as well; his use of meditation apparently helps him deal with it, along with constant exposure to mild-to-excessive pain giving him a very high threshold for pain, and it may also explain why he always seems to be in a bad mood and how, though he can survive it, he doesn't collapse whenever he takes a few hundred rounds to the chest and face). The problem of why the backs of his hands, where the claws come out, don't each have three holes is explained by his claws actually punching a hole through his flesh every time he extends them, at which point his Healing Factor closes the wounds before he bleeds all over the place. Just where all the mass of his body comes from when he heals from massive injury (for instance, all of his organs and flesh tissue, aside from his brain and skeleton, more than once), however, is completely ignored. As is why his bones don't fall apart when everything that's not bonded with adamantium is completely destroyed. He does tend to wind up naked when that happens, though, at least.
It isn't COMPLETELY ignored actually...it probably wasn't Claremont's, but there was a short arc in which Logan, while travelling through a desert, catches and eats raw a crow (he feigned fainting to let the birds approach) after a hallucination he was having (long story) reminded him that his healing factor needed proteins in order to regenerate tissues. For regeneration of far more severe injuries, another explanation has been given in another comic: Logan had...ahem...defeated the Angel of Death in a duel (he didn't know who the guy was though) and had since then been granted a sort of "immortality" (his healing factor was able to heal him from ANY injury). At the end of the arc, Logan had his "pact" with the Angel canceled and was informed that, from that moment on, his healing factor was going to be far less effective.
He's got to have superhuman strength (or close to it) to be able to be agile at all while carrying around a skeleton that weighs around a hundred pounds, Depending on the Writer, more than a normal human's. Possibly the result of his healing abilities building more efficient muscles, since he was pretty quick relatively shortly after receiving his adamantium, or a combination of that and training while lugging around so much weight.
One description of his healing factor indicates that he has unlimited stamina - due to constant regeneration, his muscles never tire from overuse. Thus Wolverine is granted a degree of superhuman strength from constantly training and fighting with 100 extra pounds of adamantium to haul around. Also, human muscle is much stronger than one might think, but using it to its full potential would result in muscle damage and liquefaction. Wolverine's healing factor means he can use his maximum theoretical strength all the time. Combined with unbreakable bones, this means Wolverine can also lift objects much heavier which a normal human otherwise could with their own muscle strength at peak athletic levels, but cannot in reality due to their bones snapping from the pressure.
Wolverine's healing factor even extends to his mind. As stated in the trope description, super healing doesn't account for a mind being overloaded with pain. Wolverine's healing factor, however, compensates for this by cutting out the most traumatizing memories (both emotionally and physically). This can be interpreted as meaning that the reason Wolverine is able to withstand such devastating injuries because his brain cuts out all trace of the trauma, much the way the brain in Real Life averts Dizzycam by inducing temporarily blindness whenever the eyes move.
This has been given as one possible reason why he will never fully recover the memories that he had before his adamantium implantation: his healing factor is preventing him from recovering those memories because they would be too emotionally painful.
Despite the "protein" point above, he once survived, when trapped under a glacier for six months, by eating parts of himself.
Alternately, the lack of hayflick limitations could be part of his primary power (the telomeres simply heal like everything else instead of degrading with divisions), which would make the required secondary power some sort of alternate storage mechanism for the information in his DNA, used to repair that DNA when damaged.
Banshee's hearing is extremely powerful. According to him, with powers like his (sonic powers), the alternative would be being deaf.
In Ultimate Fantastic Four, Sue Storm lampshaded the impossibility of her powers, pointing out that there's no conceivable reason why she should be able to see things while invisible. Luckily, she's a bio-geneticist and thinks the mystery is fascinating. And during his time on the book, Warren Ellis spent pages and pages justifying the Team's powers.
Reed isn't even strictly human anymore (to the point where he doesn't even need to eat), as his organs have been replaced with a hyper-efficient bacterial stack that bends and twists with his body.
Johnny is a living nuclear reactor that achieves perfect fission using his body's fat cells (which gets him into trouble, as he initially doesn't eat enough to support his powers and ends up in a brief coma because of it).
Ben is literally the Ultimate Life Form, with limitless strength and the ability to survive any environment... but the adaptation to do so means that his body obeys the Square/Cube Law and is super-dense as well as incredibly large (nine feet tall and in the neighborhood of eight tons), which is why his craggy "Classic Thing" appearence looks the way it does.
Presumably the goggles interact with invisible radiation — UV and infrared — while still magically being totally transparent to visible wavelengths.
Even in Marvel Classic, Sue's Force Field isn't permeable to air, and the limited air supply is used both offensively and as a limitation when she's using it for protection. Like nearly everything, this is Depending on the Writer.
In Marvel Adventures Fantastic Four #26, the Silver Surfer reasons that she can make her force fields porous enough to allow air for her to breathe. He takes full advantage of this when he defeats the Four by overloading their powers, causing her to nearly suffocate.
Sue's invisibility is explained in the Main Marvel Universe. She extends a light-bending field around herself and her immediate area, which is what renders her body and clothing invisible, and she can extend this to other people or objects if she wishes. As for her vision, remember that she can see other things that are invisible—whether it's under her power or not. Her eyes can perceive wavelengths of light that normal humans can't, and it's through these wavelengths that she can see while invisible. Again, Depending on the Writer.
When Stan the Man created her, he might have remembered that Marvel had already done this story in Tales To Astonish earlier the same year, lampshading this problem with invisibility. Maybe if he had we wouldn't have all these Flame Wars today regarding Sue's eyesight.
In fact, the original letter that detailed the Fantastic Four and their powers was reprinted some years back in a special issue. Sue's eyesight is not mentioned, but she was permanently invisible and unable to make anything else invisible, even clothes. This was nixed because Sue taking off her clothes on-panel was deemed too sexy.
Fantastic Four's Human Torch has the fireproof skin/lungs/etc. secondary power.
In The Ultimates, mutant Quicksilver had a Required Secondary Powers battle against Hurricane, an enemy speedster who'd got her powers from advanced surgery, and who wore a reinforced suit designed to resist friction. He grabbed her and started accelerating. Her skin burst into flames around Mach 4 or so, and she completely disintegrated moments later. So much for the suit. Quicksilver, whose mutant power includes all required secondary abilities needed to move at an acceptable fraction of the speed of light, reminded her smoking body that he'd been easily hitting Mach 10 since he was a teenager. The moral of the story: if you fight someone with the same primary power set as you, make sure your Required Secondary Powers are up to their standard.
The Marvel-616 version of Quicksilver once remarked that his body efficiently processes all his food, giving him the energy to run, and that his feet are designed to withstand the impacts of repeatedly hitting the ground. Pietro's enhanced physiology also gives him Made of Iron qualities and makes him far more durable than he looks, as a body capable of withstanding the stress of traveling unprotected at the speeds he hits would need to be immensely tough. This frequently comes up when he's attacked by someone who assumes he's another Fragile Speedster only to be surprised when he shrugs off what should be a devastating blow.
Quicksilver's sort-of-nephew, Tommy / Speed of the Young Avengers, got a job assembling circuit boards at super-speed at one point. He chugs some coffee, turns into a blur, and then tells Prodigy that from his perspective that was about a week.
Archangel of the X-Men has the increased strength and stamina necessary to fly with a gigantic honking wingspan. His wings themselves are also strong enough to slap a grown man across a room, or break many bones at once.
His actual wing surface area isn't nearly large enough to lift a human-sized body using real-world physics— ever wonder why hang gliders are so big? So Stan Lee gave him a required-power weight loss by attributing zero body fat and hollow bones like a bird— except that doesn't work out either, the largest birds have proportionately a lot more bone per body volume than even the smallest human, let alone a six-footer like Angel, and hollowing his bones only shaves off a few pounds of weight. Likewise, a man of his athletic build and muscle mass normally has less than ten percent body fat anyway, not nearly enough savings in weight, especially with such a high proportion of dense muscle.
He also presumably has a more efficient oxygen absorption system (Birds have vastly superior lungs to mammals) although it is never stated
One power of Archangel's that seems to come and go Depending on the Writer is that his blood has healing properties, meaning he is able to grant people a temporary healing factor through a transfusion. This must mean that he is a universal donor since he has yet to kill anyone with an immune system reaction.
Assuming the healing factor doesn't just change the blood.
Along with his super-efficient lung capacity his tolerance to extreme wind conditions and cold at high altitudes (he's been shown casually hitching rides on airplanes for long distance travel and having no problems with the thin air, cold, or high velocity airflow) also ends up forgotten by many writers.
Kitty Pryde of the X-Men apparently could not breathe while phased (because the air was out of phase with her) let alone breathe when inside solid objects, and yet for some reason should could still walk (and not drop straight through the center of the earth whenever she phased), presumably because she could create some sort of phase boundary between the soles of her feet and the ground that allowed the ground to continue to hold her up against gravity. This was entirely implicit until Grant Morrison's run, when for instance, Kitty could often be seen climbing air (using the same boundary effect) and could breathe while phased in open air at least (because she can phase the air around her the same way she phases her clothes or people she is holding.)
Similar assumption can be made that Nightcrawler can extend his teleportation outside the limits of his body: if he didn't, every time he used his power his clothes would drop off. Since the film version of Nightcrawler can take another whole person with him if he is in direct contact when teleporting, this seems to be fairly plausible.
Cyclops of the X-Men is probably one of the best billiard players in the world. Why? Well, eventually somebody realized that the absurdly complex ricochet effects he pulls off with a moment's thought using his eye-beams must mean he has some kind of sixth sense for angles and geometry. So now he does. Not necessary, but necessary for him to be able to use his powers the way he does.
According to The Physics of Superheroes (by real-world physicist and comic book fan James Kaklios) Cyclops must also have super strong neck muscles, as the beams are described as concussive force - without such musculature, Newton's 3rd law says his neck ought to be snapped every time he uses his powers. Not sure how accurate this logic is, though.
The Word of God is that he feels no recoil at all, since the "push" for his eyebeams actually comes from another dimension. He's just the doorway for the particles that make up the beams.
Of course, the first time he activated his powers was to use the recoil to slow his and Alex' descent to the ground from the plane they jumped out of.
Alternatively, there is a minor meme going around which proves Cyclops can fly. The eyebeams produce kinetic kickback, but he is immune to this kinetic energy. If he only held his hand in front of his eyes, then WHOOOOSH.
Something similar happened with Bouncing Boy from Legion of Super-Heroes, 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 & mathematics, so he became one of the Legion's main science guys & rarely used his primary power. Thankfully.
And he was a great billiards player- he knocked three balls into the nets with one strike!
Colossus in Ultimate X-Men can turn his body to steel. It was later revealed that he has no natural super strength to compensate for the added weight of a metal body and instead dopes with a power-magnifying super steroid.
The Ultimate Galactus trilogy also has a bit where Sam Wilson realizes that if Colossus turned his entire body to organic steel, then he wouldn't be able to see. One eye poke later...
Ultimate Pyro is able to generate flames, but he is not immune and is covered with gruesome scar tissue as a result.
It was even worse for non-Ultimate Pyro, since he could only control fire, but needed a special suit to generate flames (which was likely also fireproof).
Another X-men subversion: Armor is a force field user whose force field is invulnerable to most forms of physical and energy attacks, but is vulnerable to lasers specifically because it has to let light through. Incidentally someone once tried the same trick on Sue Storm. Once.
Marvel's Taskmaster can achieve limited Super Speed if he copies the moves from fast-forwarded video, but he can only use it in small amounts, since he does not have secondary powers to compensate for the fact that it strains his body.
He also lacks certain required secondary skills - for instance, when he was young, he copied a professional diver's dive. But neglected to learn how to swim first.
Taskmaster is a bit of an odd case; he supposedly has no superhuman powers beyond his signature "photographic reflexes", yet is not only able to pull off the aforementioned feats, but also Spider-Man'sspeed and agility, and further, can catch bullets, leap dozens of feet vertically, casually send a man flying with a punch and shake off getting smashed through a reinforced wall by the force of an enraged Spidey (thinking Taskie had kidnapped Mary Jane) kicking him in the head.
Eventually, it was shown that every time Taskmaster memorizes a new set of moves, he loses a bit of memory, including things like his real name. While this isn't how memory works, it may explain why he's able to do Spidey's moves. If his brain is constantly compartmentalizing, it may be able to shut off the parts of the nervous system that would cry out in pain when attempting a crazy maneuver, while increasing adrenaline output (á la mothers lifting cars off of their children, also an Urban Legend).
Considering not all super powers are innate in the Marvel universe, its possible the reason Taskmaster can do more then should be humanly possible is that at some point he copied a Mystic Martial Artist and is useing some sort of chi or other mystical force that normally requires years of training to achieve
Ultimate Marvel's version of Reed Richards has his body transformed into an undifferentiated "bacterial stack" with no internal organs or tissues, so he has no need to worry about, for example, his stretched arms going numb because his heart had to try to pump blood the length of a football field. How he gets energy without eating is glossed over.
Note that this is roughly the power of Plastic Man. Nothing new under the sun.
They also use this to explain, both in classic and Ultimate Marvel, why Reed Richards, who didn't think to account for cosmic rays in his experimental rocket design, is now the smartest man on earth. His stretchy powers allow him to morph, stretch and contract his brain in ways that make a smart guy even smarter. Though this does clash with the "undifferentiated bacterial stack" explanation.
Daredevil is occasionally shown having to deal with the sensory overload that comes with his powers, especially regarding hearing and sound. Notable examples are loud sounds or concussive blasts (like from an explosion) disrupting his sonar and causing him pain, and having to sleep in a soundproof isolation chamber.
In The Movie, he's shown sleeping in a sensory deprivation tank, which closes and opens according to a timer.
A subversion comes when he fights Bruiser, who can shift his center of mass to make himself super-strong or make it difficult for Daredevil to flip him. Using his radar sense, Matt can detect that Bruiser's body can't handle the changes to his body made by the power, so he concentrates on one shattering bone and hits it, escaping from Bruiser.
Iron Man villain Ezekial Stane, the so-called "Iron Man 2.0", has bioengineered himself in such a way that he can fire repulsor blasts using his own bioelectricity, increases his healing, and so forth. However, he has to consume a very high calorie paste in order to keep his blood sugar up, and his armor chiefly acts as a way to vent heat from his body, as he hasn't figured out how to keep his flesh from burning off.
John Byrne's Next Men series has a super-speedster who runs barefoot— his body can stand the speed, but shoes wear out in seconds. Even at that, he still had to spend months toughening up his soles to avoid crippling blisters. One of his teammates has superstrength, but needs a special exoskeletal harness to dampen his powers or his body can tear itself apart, not to mention destroy everything he touches. Although his hyperdense bones and muscles do save his life when they limit the penetration of bullets, saving his vital organs. Scanner gets super-vision, but his eyes become huge and all-black to absorb all those frequencies and he needs to wear a special filter visor to avoid painful sensory overload. The invulnerable woman couldn't cut her invulnerable fingernails or hair, and her skin was slowly turning chalk-white as ultraviolet light stopped causing tanning (a minor research miss, as tanning is made up of two processes, only one of which is a result of UV damage).
The New Universe paid a lot of attention to this trope, as part of its pitch of being more realistic:
Minor villain Skybreaker could fly, but had no other powers, so he required a special suit to protect him from wind, friction, high-altitude cold, and to provide oxygen. It also has navigational gear, since there are precious few road signs at 40,000 feet.
Food was the lesser problem. Apparently, his body is potentially much faster than his mind, so he can't get a restful sleep if not under tranquilizer (or a teammate's energy draining power). And the constant vibration caused by lesser muscular movements cause him to be mildly destructive when touching things. Or opening Coke cans.
Deadpool's Healing Factor only works because he has such severe cancer that his body is constantly regenerating lost cells. He just makes it regenerate more when he takes damage. He actually weaponizes this when the Skrulls want to make an army of clones with him, and gives them the healing factor, but not the cancer, causing them to mutate and die.
However, while he has to ability to regenerate tissue, there is no guarantee that it will regenerate right. Once he broke multiple bones and his assistant strapped him to a rack in order to ensure that they would heal straight.
It's possible that Spider-Man's super-strength is a Required Secondary Power. Everything else —agility, wall-crawling, advanced nervous system— falls under "proportionate powers of a spider" but spiders aren't really known for their brawn. It does, however, probably keep him from dislocating his arms when he leaps from a great height onto the side of a building.
Spiders, like ants and many other insects, have a muscular system that is actually built on the same principles as hydraulics. How Spidey pulls off hydraulic-based strength without massive physical mutation, however, is anyone's guess.
Lampshaded on at least one occasion when Spidey loses his powers but still has his web shooters; he tries to swing away but lacks the strength to hold onto his own web!
Another embarrassing moment had Spidey lose his Spider-Sense and having it revealed that he uses it to make sure his webline doesn't hit anything that could break it, like a loose piece of a wall. He hits one and embarrassingly slams onto the hood of a police car.
Most comics allow normal-strength people to hold their own weight on one arm for some reason, it's interesting that writer remembered. Another didn't, and had him able to web-swing fine with his powers gone, except without his spider-sense he had to actually concentrate on things like aiming.
Spider-man's super-strength is not a Required Secondary Power at all; he's always been presented as having the proportionate strength, speed, and agility of a spider. It all stems from the same simple concept: a misunderstanding of the Square/Cube Law.
Technically, since Spider-Man's origin was retconned from "radioactive spider" to "spider with an experimental retrovirus" his powers aren't anything to do with the spider at all, they're side effects of enhancements that the lab was trying to make to a spider. Spiders don't have a 'spider sense', for instance, which is the required secondary power for all of the things he uses his strength and agility to do.
Non-organic webshooters require him to have the chemical and mechanical engineering skills to build them. In The Amazing Spider-Man, the fluid is organic, just compressed, and he builds a way to deploy it. In some versions, the formula came to him as part of his powers.
The Eternals are powered by cosmic energy flowing through every cell in their bodies. This makes them able to do things like fire Eye Beams and use Super Strength, as well as powering their Psychic Powers, but dispersing all the resulting waste heat is quite a problem— they tend to stick to cold places like mountaintops and the middle of Siberia for just that reason. Gilgamesh even went into a coma once fighting a lava monster— and before that, he had to go into a motionless trance just to survive in a hot cavern while guys like Captain America and Black Panther just stood around and sweated. The laws of thermodynamics are a harsh mistress.
Chamber from Generation X is a triple subversion: he doesn't need to eat, breathe or drink thanks to the pure-energy furnace within his chest, which is a fortunate thing since the same furnace blew off his jaw and a good portion of his chest when his powers first surfaced. With no lungs or mouth, he can't talk normally but then he develops a secondary mutation of telepathy to communicate with others. As it turns out, he doesn't need telepathy; he has the potential to reconstitute his missing parts but isn't skilled enough in his powers to do so for long. He nearly died in Decimation when he lost his powers and suddenly needed things like food, water, and oxygen again.
The secondary power of "can tolerate cold temperatures" is memorably played up for three X-Men at once in an issue of X-Men Unlimited, while a team of Storm, Iceman, Colossus, and Angel are on a mission in Antarctica:
Storm: Hmm. Angel, my weather powers protect me from the chill, Colossus is immune to extreme temperatures while armored, and Iceman is, well, Iceman. How are you doing?
Angel: I'm very cold, thank you for asking!
Which is a bit of research failure regarding Angel, since he's adapted for extreme heights that actually includes an ability to handle frigid temperatures.
Mystique, an X-Men villain shapeshifter, can copy the appearance of other people down to fingerprints, voice and retina patterns closely enough to pass biometric scanners. In addition to the Photographic Memory required to remember all this perfectly, she must have some kind of ESP to detect such things in the first place just from a brief encounter. She's certainly never shown scanning and studying the retinas of people she is going to copy.
It was shown in her side series that she requires a minimum of eight words to adequately mimic someone's voice. How this allows her to pick up speech idiosyncrasies is anyone's guess.
The Punisher 2099 once tracked down a techno-shaman who had encased himself in an impenetrable force field to protect himself. Punisher figured out that it still had to be able to exchange heat through the field, and fried the guy inside the force field by showering it with hot plasma.
Red Hulk becomes hotter the madder he gets, allowing him to burn and melt things just by touching them. He suffers his first defeat when he becomes so mad that his own heat hurts him.
When John Byrne took over writing and drawing West Coast Avengers, he came up with the theory that the probability-altering powers of the Scarlet Witch must actually require the power to rewrite all the history that goes into creating probabilities, thereby turning her into a Reality Warper.
In one story set in Captain America's early days, it's revealed that when he decided to take up shield slinging as a method of attack, he had the strength to pull it off, but not the math skills to make it fly true. It took him awhile to do it.
As pointed out by Cracked, there's quite a few of these not already listed:
Storm's lightning bolts don't come from her body's own internal energy supply, since she'd have to constantly be scarfing down food just to make up for the calories she'd lose every time she used her powers. This means she's either drawing electricity from the air around her, or is simply generating it from out of nowhere, both of which are extremely impressive.
Sandman can control his own sand, making it fly and move around, including turning himself into a cloud and controlling his own direction of flight (so he's not using the wind), so Sandman clearly can fly.
One character in Global Frequency has a cybernetic arm with superhuman strength, and goes into detail about all the secondary modifications that had to be made to her body so she could use it without ripping it out of its socket or breaking her own back.
Member 436: I have to be careful with it. Bioelectric enhancements are cranky. It's not a case of just sticking an artificial arm on. The surrounding bones and fibers have to be hardened and supported, or else the new arm will rip clean off your shoulder the first time you flex. You'll need tensile support across your back, or your spine will snap the first time you lift something heavy. You need new skin; human skin isn't tough enough to handle the subcutaneous tension of superhuman strength. You'll take a chip in your brain to handle the specific dataload from the artificial nerve system controlling the arm. You're getting the idea, right?
And all of the above is mentioned just to suggest to the rest of the team (and the reader) how thoroughly the Tragic Villain of that issue, a full Hollywood Cyborg, has been rebuilt and how little of him can be called "human" anymore.
In the Valiant ComicsSolar, Man of the Atom, Solar encounters various empowered people, some with no secondary ability to compensate. One petite woman has super strength, and a level of invulnerability, but no anchoring ability. So if she threw a punch forward, the reaction would in turn throw her body backwards. She fixed this by wearing a vest weighted down with depleted uranium. This also kept her from hitting the ceiling every time she took a careless step.
Empowered tried to pick up a car, but succeeded only in tearing off the fender. She did manage to pick it up and throw it on her second try, with more careful hand placement, but...
"Aaa! M-my BACK! Oww... I think I pulled something...!"
Then she figured out that drivinga car into her enemies is easier and has more force to it.
In Irredeemable, Plutonian, being a Flying Brick, should need several of those to be able to use his super strength the way he does, like lifting ships without them breaking apart, but he doesn't, because he doesn't have primary powers either - he is a Reality Warper who subconciously alters the fabric of spacetime around him. When he punches something, he changes the density of his fist and the objects he punches and breaks Newton's laws to not outright kill his opponents. He isn't even aware of it, he just thinks he is very strong.
Max Damage, from Irredeemable's sister title, has super strength and invulnerability which proportionally increase the longer he's been awake. Unfortunately, a side-effect of the latter is that he loses all sense of touch, taste and smell after a couple of hours - he describes it as being numb instead of being tough, like God didn't know when to stop with the Novocaine. He also suffers from the normal effects of sleep deprivation, which is sometimes necessary to get his powers up to a certain level, so the stronger his body becomes the weaker his mind gets.
A minor character from Rising Stars was Nigh Invulnerable, but didn't have several secondary powers that usually come with it - he had no enhanced senses so his powers blocked his sense of touch, pain and temperature and he had no super strength so he was rather useless in a fight, being beaten like anybody else, just without feeling anything. And he needed air just like anybody else, so he was suffocated to death with a plastic bag. In fact, lack of enhanced senses was what killed him - without his powers he didn't feel it when the murderer tied him up and put the bag on his head.
Butterball, from Avengers: The Initiative has similar problems - his powers made him frozen in the (quite obese) form he was when they activated, which means he cannot realize his lifelong dream of being a superhero because he can never train and get in shape for crimefighting and he doesn't even have muscles necessary to fight in a way the likes of Blob do. Of course the Initiative could use their nanotechnology to block his powers and then train him, but their chief scientist was really a Skrull and he used his position to kick him out.
Also relevant is Citizen Steel of the Justice Society of America, who is super strong and invulnerable to harm but has an extremely stunted sense of touch as a side-effect of the treatment that gave him his powers. It's to the point where 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 had to be cast around him to bring him down to a level of super strength where he could actually function without destroying everything.
Image character Brit also has nigh invunerability without super strength, so his way of fighting super-strong villains was to let them throw him at nearby buildings and make them fall on their heads, until he got himself pair of strength-enhancing gloves. Later, he also started using a Jet Pack.
The Savage Dragon averts the typical Healing Factor trope of bones automatically resetting themselves as they heal. A foe once beat Dragon until nearly every bone in his body was broken, then stuffed him down an industrial chimney, forcing Dragon's healing factor to repair all those bones (and, presumably, whatever muscle and other tissues damaged along with them) in the wrong positions. Despite this, Dragon managed to climb out of the chimney and even (briefly) get into another fight before being discovered by allies and receiving medical treatment. The worst part? One of Dragon's super-strong friends had to re-break all the misaligned bones so that doctors could re-set them properly.
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.
Deconstructed in the Donald Duck comic "Super Snooper Strikes Again!" by Don Rosa. Donald briefly becomes a Flying Brick after chugging down some Applied Phlebotinum, and makes several attempts to impress his nephews with his new powers. He tries to travel around the world in an instant, but realizes that he still perceives the passage of time normally despite everyone else effectively being frozen in time while he's moving around at Super Speed, so the task could take him several months or even years to complete, and nobody would notice anyway. He also tries to use his Super Strength to lift both a mountain and a sunken cruise ship, but the mountain starts falling apart at the base and the ship breaks in two due to years of rust decay to the hull.
Subverted horribly when a little girl who's invulnerable to everything, including germs, has her powers temporarily disabled. Because her normal immune system has never had to do anything before, it's far too weak to fight even a minor infection, and since the doctors are unable to treat her once her powers return, she winds up dying from a normally nonfatal and easily curable disease.
The teacher Miss Kyle has the ability to increase the density of her body, which makes not only her muscles stronger, but her tendons, bones, skin, etc. as well. Because she has no shapeshifter baggage, though, her size decreases at the same time. It was stated somewhere that she normally has a small amount of density increase at all times, converting a beautiful but petite woman into someone a little more than average.
The Gym coach, aka Rockside, is a brick literally made of stone. He can't find a sneaker that can stand up to his weight and hence has to walk barefoot.
Harold Nelson's powers include being able to weaken or strengthen other people's superpowers. When used offensively he can increase people's powers beyond their control and potentially beyond the capacity of their requisite secondary powers to contain; this can be painful, inconvenient, or deadly (the girl who dies from infection example was a case where he shut down her powers for half an hour).
The comic reboot of The Six Million Dollar Man, The Bionic Man eliminates the Required Secondary Powers that his television predecessor (and other similar characters) had to have to explain why, when lifting a car with their single bionic arm it didn't do bad things to their otherwise entirely human torsos: in the new setting, the bionics go through their entire bodies, allowing them to use Super Strength without breaking their spines.
2000 AD: The Visible Man shows at least one such problem with invisiblity. The protagonist's skin becomes invisible so that all his internal organs are showing, making him look like a monster and becoming a target for unscrupulous scientists who want to perform all sorts of nasty experiments on him against his will. After he escapes from his confinement he tries to restore his skin's appearance by developing a suntan. He quickly discovers that because the light rays go right through his skin and musculature they simply burn his organs, so he's forced to find a different way.
Gruesomely demonstrated in the superhero-genre Deconstructor Fleet title Über, in which one of the British supersoldiers-under-construction tries to show off his superstrength to impress a girl before his superdurability has caught up with it - when he exerts himself to his full strength his muscles rip completely away from his skeleton and he dies horribly.