The dragons from Dragonriders of Pern generally range from 20 to 42 ft. long, with wingspans not anywhere near large enough to support that much weight in flight. Much later in the series, it's retconned that they're instinctively using telekinesis to help out the flight process. Since their telepathic and teleportation abilities were known long before this, it's not a huge leap.
Also, their bones aren't of the same material as Terran animals' bones: lifeforms of Pern have some chemical differences (notably being high-boron), and dragons were engineered from native creatures.
Though the native creatures were far smaller, throwing the Square/Cube Law right out the window. Though since Kit Ping Yung, the creator of the dragons, was stated in the book to be the only geneticist smart enough to be taught the Eridani secrets of gene manipulation, it's entirely possible she enhanced the telekinetic properties of the fire-lizards to make up for this.
Important plot points in some books rely on the fact that teleportation is a dangerous business; as suggested in the article it is possible to accidentally arrive underground and be entombed in stone.
Similar to Pern, the Eleint Soletaken of Malazan Book of the Fallen are able to transform into massive dragons. However, the sheer size of their new forms means that half of their flight relies on sorcery and if their wings are damaged they need to rely almost solely on it to stay airborne.
H. G. Wells's The Invisible Man needed to walk around naked to use his power, and had to avoid eating beforehand, so that digestion wasn't visible. Also, his corneas weren't actually invisible, just really, really hard to see due to some partial invisibility and small size. His eyelids, on the other hand...
Note that the nudity requirement wasn't actually necessary, as Griffin's process worked on white fabric as well as living creatures. He just didn't think to create some invisible clothes for himself before smashing his equipment and becoming a fugitive.
Lampshaded in the Chevy Chase movie, Memoirs of an Invisible Man, wherein the main character sees his own stomach activity in the mirror and is so disgusted that he throws up. He later is told by his love interest that she understands why he missed their dinner date. His response: "Trust me - the last thing you want to do is watch me eat." Also, smoking lends itself to some interesting effects, and he becomes semi-visible in the rain. However, the suit he was wearing during the industrial accident is also invisible, meaning he doesn't have to go naked as long as he keeps it clean. He later has said love interest teach him how to apply make-up so that he can interact with society in at least a semi-normal fashion.
Somehow, the question of whether his urine should also be visible never seems to rate a mention...
In the H. G. Wells short story The New Accelerator, which features a super-speed serum (probably marking its first use in its modern form), not only predicts today's doping scandal by mentioning that the stuff could be used to cheat in fencing, but also has the characters suffering vertigo while the serum takes effect, not being able to run without beginning to burn up, leaving footsteps of burnt whatever-they-step-on wherever they walk, and in one instance being unable to keep objects perfectly still, so that a little dog goes flying across a field. While talking about the serum (which is when the cheating was brought up), the characters talk about the consequences of using the serum over long periods of time, namely accelerated aging and appetite. The only thing it misses is they should be walking like they're on the moon.
The Required Secondary Powers necessary to use the magical gadgets of folklore and mythology are acknowledged in some of the Rincewind novels of the Discworld series. For instance, seven-league-boots exist, but using them requires extensive magical protection and preparation, since having one leg miles ahead of the other causes an awful groin sprain.
In the Midnighters series, one of the characters incredible leaping abilities in during the 'blue hour' translate to leParcour in normal time because of his innate sense of physics.
In David Eddings's Belgariad, when you use magic to move an object, the resulting force is the same as if you had physically touched the object - so you have to brace yourself with equal force, similar to tightening up your muscles, or some such. The main character learns this the hard way the first time he tries to move a giant stone, as he ends up buried up to his armpits in the ground (he tried to push it up instead of merely sideways).
The protagonist's mentor scolds him and comments that if he HAD tried to push it sideways, he'd likely have been thrown across the continent by now.
This is also used as an explanation for why certain magical effects are not used very often. For instance, changing the weather is not a normal effect, because it requires moving vast amounts of atmosphere around.
Something similar to Belgariad also holds for magic in Discworld. A wizard who wants to move a large weight telekinetically needs to harness some secondary force to avoid being crushed by the mass he's lifting; e.g. in Light Fantastic, a wizard levitates himself by dropping a weight off a roof and transferring the force to himself. This rule seems to be often ignored if it would get in the way of the story, however.
If attempting something like this without such an exchange, they have to use their own mental skills to do so, with a related physical cost... avoidance of which is described as (paraphrased) "preventing your brain being flicked out your ears". One example is in The Last Continent, where a mathematically-inclined wizard spends some time working out a long-distance teleportation spell to account for angular momentum (which they end up dumping on a kangaroo, since it has to go somewhere).
The math for this infuriated the senior staff to no end in Interesting Times, where Ponder Stibbons insisted that, since the Disc is constantly revolving, they had to find an object of similar mass to Rincewind to trade him with during teleportation, otherwise either he would end up smeared all over the destination, or they would receive something at terminal velocity in their Main Hall. It worked out reasonably well the first time (he traded with an iron cannon on wheels, which did no damage on arrival, while he splashed into a convenient mound of snow) but the retrieval accidentally resulted in a triangular tradeoff between Rincewind (arrived with zero momentum,) the aforementioned cannon (ditto,) and the very, very unfortunate kangaroo mentioned above.
Not to mention Eskarina demonstrated teleportation without an "anchor". Part of the Discworld narrative causality is things can be possible as long as you aren't told they aren't.
Directly stated in the Wild Cards series of novels with the beautiful (and winged) character of Peregrine. When a boyfriend tells her he hates mutated "Jokers", she explains to him that she is one. After all, her wings are large deformities that are not the source of her flying ability, she does that psychically.
The Wild Cards criminal Fadeout bends light to become invisible, and is effectively blind while doing so. He can only see by making his eyes visible.
There's also a Deuce with the ability to produce flame from his hands. Normally this would make him an Ace... except for the fact that he's not immune to his own fire.
And then there's Kid Dinosaur, who can change into any dinosaur he wants...but he can't increase or decrease his body's mass. So he can become a T-Rex, but the T-Rez is only 4 feet tall.
Heretics of Dune sees Miles Teg gain Super Speed, but needs to become a Big Eater to compensate (several characters lampshade his Big Eating). He also gets his hands badly bruised and torn from hitting his enemies at such speeds.
In the The Shahnameh, written by Ferdowsi of Tus, the main hero, Rostam, at the beginning of the story is too strong to walk, since with every step he would ram his leg into the earth up to the waist. He had to pray to his god make him weaker to actually be able to walk normally.
Tuck Everlasting is probably the first children's book to examine Who Wants to Live Forever? in detail. It's never explicitly stated that the characters can't die in any way (other than a brief anecdote of Jesse surviving a fatal fall), but this is implied to be the case, given the Tuck household's being located squarely on Dysfunction Junction and the fact that none of its inhabitants have offed themselves in their roughly 100 years of immortal life thus far.
In Maximum Ride, the eponymous winged girl, and her friends, were genetically engineered so as to have these necessary powers, so to speak. They do have Birdlike bones, and are definitely Big Eaters. They also happen to be super strong for some reason.
Probably because their wing muscles had to be built using a more efficient chemistry than human muscle to make them strong enough to lift a human-sized body without a heavy load of muscle mass, and as long as you're doing the wings, hey why not buff the whole body as well.
Corran Horn can manipulate energy in any way he desires, but he has to find some output for it. Interestingly, this is the only way he can perform psychokinesis, so Corran is one of the few Jedi who actually obeys the laws of thermodynamics.
In Timothy Zahn's The Cobra Trilogy, the eponymous Cobras are commandos whose bones have been covered with a practically unbreakable ceramic laminae, whose joints have been augmented with servomotors, and who have been implanted with a power source, concealed energy weapon systems and a computer to help them control everything (which also provides a library of preprogrammed "combat reflexes", shortening training time). In the first book, the initial crop of training injuries are skin abrasions and subcutaneous bleeding caused by not possessing Required Secondary Powers for super strength. It's eventually discovered that Cobra modifications inevitably cause anemia, arthritis, and (believed) immune system deficiencies. (The books are devoted less to combat than the peacetime ramifactions of wartime decisions... incidentally, Cobra recruitment is still going strong by the end of the trilogy, two generations later.)
Jack Fleming in PN Elrod's The Vampire Files can turn invisible and (mostly) intangible, but he's unable to see in that form.
Harry Dresden gets badly screwed when a vampiric sorceress works out that the force fields he uses so much block force, but not heat. Two of her goons break out the flamethrowers, and while the shields block the napalm itself, the heat roasts Harry's hand and renders it nigh-useless for several books. When he finally gets around to making a new shield bracelet, he hits the books with this trope. The new shield protects against everything, even things like sound and electricity, but this has the drawback of using more of his energy.
Similarly, kinetic energy is still transferred to Harry's shields; objects that hit the shield rebound off it, but momentum is still imparted to him, with the force evenly distributed throughout his body, which means that a sufficiently powerful blow can send him flying. He actually takes advantage of this once by catching the force of an explosion on his shield and using it to propel himself out of the blast zone, as his shield would have given out had he tried to withstand the explosion directly.
Harry also points this out himself when dealing with potions. While he can make a super-strength potion, he'd also need to make a corresponding potion to deal the damage having said superstrength would deal to his body. The issue with that, of course, is that mixing potions, like mixing any other drug, is a bad idea.
Sometimes this trope is the loophole that Harry uses to get himself out of impossible situations, especially when motorcycle-jousting with a limo.
Overall, the series as a whole very strongly obeys the laws of physics, which seems odd for a series where magic is real. Basically, magic is only how an effect (like a blast of wind or fire) is produced. Once the effect is summoned or otherwise put in play, it will obey normal physical laws from that point on.
Harry goes on a rant once when a fireball in totally-not-D&D stops at a precise distance, rather than move like fire should.
Also, while there are a number of beings with superhuman durability, they still weigh the same as they normally would, so a human-shaped being will still only have human mass, and can be thrown around by impacts or one of Harry's force spells even if they aren't actually injured by them. Similarly, superhuman strength and speed don't do any good without a surface to push off against, so unless they have wings, supernatural beings can't change direction while in midair, something Harry has taken advantage of several times.
Harry isn't the only one that runs into problems with this trope. For instance, after becoming the Summer Knight, Fix has the ability to throw fireballs of Summer Fire at his opponents. In Cold Days, he gets caught in the crossfire between Harry and someone else who can throw around Summer Fire. It's implied that this would have killed Fix, but even if the heat didn't kill Fix, the lack of oxygen (from the fire consuming all of it) certainly would have.
In Soon I Will Be Invincible, Dr. Impossible, a Mad Scientist, has superhuman strength and durability from a lab accident. However, he's not as strong as any of the superheroes who have superhuman strength as a power, and all his plans revolve around Mad Science rather than his own brawn. Considering that he's a Super Villain in a Comic Book-like world, Failure Is the Only Option, so presumably he would have to have some degree of superhuman strength or toughness just to survive all the times he gets thrown around, beat up and concussed by heroes.
The heroes get a good dose of this, too. Fatale is a combat-ready cyborg who needs specially crafted furniture due to the weight of all her cybernetics. Feral is a Wolverine-style genetic mixture of an ordinary human and a Bengal tiger, but his frame is such that walking on fours isn't really possible and walking on just his feet hurts. And Damsel is a Half-Human Hybrid whose parents didn't really look into how well the two genomes mix; as a result, she's stricken with regular bouts of nausea, and throws up so much her teammates think she's bulimic.
Specifically addressed for flight though. "I know that you find it counterintuitive to project wind both ahead of you and behind...but you body was not designed for high speed flight... if you do not take measures to protect yourself, especially your eyes, even relatively minor amounts of particulate matter in the air could blind you or other bring your flight to a ... terminally instructive conclusion. Adept fliers accomplish it so naturally that they have no need to consciously think about creating the shield."
Lampshaded as early as the first scene of The Runelords in which two men who each have multiple endowments of strength engage in a fight which the narrator explains is little more than "bone breaking contest" for though they both have super strength, that power does nothing to harden their bones. The books further illustrate the need to balance ones endowments such as balancing 'brawn' with 'grace', 'metabolism' 'stamina', and 'wit'.
Unfortunately, this forms a minor plot hole - the strength of ten men would be more than enough to break the bones to which the muscles were attached, let alone the strength of hundreds or thousands. Runelords do, however, have major issues with things like leaning into turns when running at 60 miles per hour, healing correctly, living their lives at massive speed whilst everyone else is normal, aging at supernally fast rates because they've loaded up too much on metabolism, etc etc. In general, Farland deals with the lack of required secondary powers very effectively. Similarly, the difficulties which occur when one loses one's Dedicates are dealt with in detail.
Not touched upon at all in Sergey Lukyanenko's Rough Draft and its sequel Final Draft, where the protagonist is erased from existence and becomes a "functional", gaining various abilities specific to his "function", in this case that of an interdimentional customs official. He lives in a water tower that links to several parallel worlds. His job is to let other functionals and normal people through, provided they follow the rules and pay their customs duties. His powers include super-strength, super-speed, nigh-invulnerability, knowledge of advanced martial arts, knowledge of all contraband items and duties, and the ability to determine what a person is carrying at a glance. At one point, he is running away at super-speed from soldiers and helicopter gunships. Nobody mentions that he should be bouncing instead of running, but he is able to zig-zag, avoiding bullets. The soldiers then take a pill that temporarily allows them to move as fast as him. The second novel briefly touches upon the functionals using advanced quantum physics to do whatever they please (something about taking pieces of themselves from myriad other worlds, where their powers are the norm).
In the Dale Brown novel Fatal Terrain, Jon Masters mentions that though the variable airframe on the Wolverine cruise missiles allows for incredible maneuverability, they have to be limited below what they can really do because pulling super high-G maneuvers causes the explosives to cook off or something and a super-maneuverable missile's a fat lot of good when it blows itself up before even reaching the target.
Honor Harrington has capabilities that are above what we would call peak human. Explained by being a genetically engineered heavyworlder. She has to pay for it with a proportionally larger appetite to fuel those boosted muscles.
Because the ability to eat all the food you want and not gain a pound is such a big downside... It is an actual problem once, when she is given standard prisoner rations for a length of time and halfway starves to death. So it's a serious problem then, but still— it's once, in 13 novels and counting.
In the novel Nuklear Age, the villain Blazer can shoot lasers out of his eyes that obscure his vision and leave him unable to see, although he somehow manages to avoid permanent blindness. However, Nuklear Man gets some of the same powers as Superman with absolutely no implications; at one point, a scientist puts him in a chamber of heat that goes up to thousands of degrees to test his powers, and marvels at the fact that even his clothes were undamaged. Presumably the fact that he draws energy directly from the stars has something to do with it.
In Larry Niven's Known Space series, humanity has developed teleportation technology that has distance and mass limits due to the Law of Conservation of Energy. Teleporting east-west doesn't generate many problems, but teleporting too far north-south generates problems because of the difference in orbital velocities between where you are and where you were. In short, teleport too far north or south, and you arrive at your destination as a human-shaped exploding nuclear weapon.
In one Dragonlance story, a group of Gnomes fly a zeppelin to the moon of Lunitari, the god of neutral magic. The inherent magic gives them powers...but not secondary powers. At first the powers are very light; one can see slightly better, one can hear slightly better, one is stronger, one can cling to walls, etc... but with prolonged exposure the powers keep getting stronger and stronger. Eventually the one with sight starts seeing through the entire moon with covered eyes, the one with hearing has to stuff his ears lest the crawl of insects make them bleed, the strong one breaks everything he touches and the clingy one just gets stuck.
Thanks to Brandon Sanderson's rather scientific approach to magic systems lots of his powers show the problems of missing Required Secondary Powers. For instance in the Mistborn series, Tineyes have heightened hearing and sight, but can be very vulnerable to bright lights and loud noises while burning. Steelpushing and Ironpulling are not run-of-the-mill telekinesis, but are based around force, mass, and their interaction through Newton's Third Law. The Kandra are a race of shape shifters with a Healing Factor who can't actually be killed by wounding them, but wounds are still incredibly painful and regeneration takes time. Also it's mentioned on a couple of occasions that a Feruchemist increasing their weight also gets their body strengthened so they don't squash themselves under their own increased weight.
The Circle of Magic series at least nods to this now and then. There's at least one seer in the series who can't control or ignore his visions and was locked up as a madman. Daja and Frostpine are noted to be lucky enough to have fire resistance, with the implication that there are smith-mages who don't.
In Animorphs, the heroes frequently come to the conclusion that the Andalite scientists who created the ability to morph into animals must have also added the ability to not feel pain as your organs and bones transform with a sickening sound.
In Star Carrier, ships moving near the speed of light (for example, Space Fighters launching a near-cAlpha Strike) generate a gravity well ahead of them to clear away dust particles and such, which would cause severe damage if struck at relativistic speeds.