Mahou Sensei Negima! - Mundus Magicus turns into one of these once the heroes arrive there - especially for those who were previously just Muggles, though the main cast remains leagues more powerful then the average thug in that world.
Wind A Breath Of Heart - In spite of seeming to be like a normal town, (almost) everyone in the town the story takes place has some kind of special power, often mundane ones, and asking what everyone else's powers are is as common as asking what someone's name is. The reason this is so common becomes a major plot point...
In A Certain Magical Index and its spin-off, nearly all of the students from Academy City are undergoing esper training. So it is reasonable to expect unnamed street bullies to have some sort of super power. As one teacher put it, a student not having esper powers is something out of ordinary and worth researching. The Superpower Lottery is very much in effect through, and most of these powers are entirely useless.
Slayers has the "anyone can learn basic magic, but not everyone chooses to do so" variant. Notably, the swordsman of the group has a high enough "capacity" to become an incredible mage, but his attention span is too short to remember or focus on the incantations.
The light novels present it a bit differently with Gourry being a bit smarter than he gives out...But double-subverted, in that his memory is STILL terrible.
Actually sort of subverted: even among the ninja villages only a relatively small number of the population ever go all the way through the academy to even become low-ranking genin. Though it does seems anyone could potentially use chakra for they various things ninja do.
Iris Zero takes place in a world where 99% of children are born with an Iris, which allows them to see visual clues. For example, one girl can see a devil tail grow on people when they lie. However, this causes a lot of problems, because living with a constant Augmented Reality really warps the way you view the world (often in negative ways). The girl mentioned above is also wears Jade-Colored Glasses and has problems trusting people. It's a world where the tropes of Kids Are Cruel and Adults Are Useless are in full play. The 1% of kids who are not born with an Iris are known as "Iris Zeroes". Main Character Toru Mizushima is one such individual, and this has made him an outcast his entire life.
Sometimes the Digimon's World borders on this trope before humans arrive in it. Digimon Adventure and Digimon Tamers added other powerless creatures so they don't count. X-Evolution the best example with no humans or anything comparable to them in sight.
Apparently, this is what happens on Earth in the Dragon Ball universe, circa Dragon Ball Online. Taking place two hundred years in The Future (well, the future of the DB world anyway), every layperson on Earth has discovered the benefits of Ki thanks to a book written by Badass Bookworm, Son Gohan. Furthermore, Krillin, Tien, and Goten & Trunks have formed their own martial arts schools based on teamwork, Ki manipulation and swordsmanship, respectively. Earthlings are so badass that when The Remnants of Frieza's Planet Trade Organization came to Earth to conquer it at one point, the people of Earth curb-stomped them with little effort. Oh, and did we mention that in this future humans and Saiyans are so genetically linked that humans can become Super Saiyans?!?note Although, you do need help from the magical dragon Shenron to do so, but still...
The actual series gives us the Saiyans, who are an entire race of warriors whose weakest members are still far stronger than 99% of the human race.
Everyone's a little bit badass in Tokyo Majin. Even the one-note delinquents in the first episode pull off improbable moves like spitting nails at a spinning bat to instantly create a nail-bat, and the nosy reporter girl can bury herself in earth like a ninja. That's to say nothing of the mystic yakuza or the five protagonists with special superpowers.
Top 10: Absolutely everyone in Neopolis from bums to tycoons is superhuman: "science hero/villains" with powers, a costume and an alter ego. Aliens, robots, gods, cyborgs, psychics, all present in the crowds. Incidental details include pizza-delivery couriers with super-speed, cab drivers "guided by the universe" and comics such as Businessman.
That is, until you get a load of the Monster Generation or even the new X-Men, whose mutations are so freakish they're pariahs even in a world full of their own kind.
In the New Krypton story arc of the Superman stories, New Krypton is a planet on the other side of Earth's sun, sharing its orbit and populated with 100,000 fully powered Kryptonians.
In an Ultimate Fantastic Four storyline, Reed went back in time and prevented the teleportation experiment by fixing the calibration of the teleporter so that Ben Grimm wouldn't have to be The Thing. The result was an alternate world with this trope thanks to the aliens they encountered on the now successful trip with Grimm being the only normal and quite happy about it. Until it turned out to be the aliens' way of killing the entire human race, and Ben had to fix it.
X-Men is a deconstruction since it shows how society would react to a growing population of super powered beings.
House of M is an X-Men story with Scarlet Witch changing the world so that most people were mutants, leaving the Muggles as a minority treated somewhat like the disabled.
PS238 focuses on a school filled with super-powered children (and faculty), and the one normal student (Tyler).
The Incredibles: Played with by the villain's objective. "And when I'm old and had my fun, I'll sell my inventions, and EVERYONE can be super. And when everyone is super...heheheh...NO ONE WILL BE." Naturally it's not this goal that makes him a villain, but everything he considers "my fun" before he gets around to it, like creating disasters for him to fix.
Although, even there, this ultimate goal is still portrayed as something dark and sinister. (No one will be special any more! It will be dystopia!)
Part of the point is that there would still be "Supers" (or at least some people more super than others) except now the Supers will be those who can pay the most instead of those naturally gifted.
Every human in Xanth has a magical talent. The power and usefulness of these talents varies wildly, from entirely pointless to world-changing. The few who don't are either immigrants or they get exiled to Mundania.
In The Amazing Adventures Of Ordinary Boy, the eponymous character is the only person in his city without superpowers.
The world of Mencu in The Crest of Zabutur series is home to the Serenghe, all of whom can manipulate at least one different element at nearly any given time.
And all the Muggles…which is most of the world’s population. Granted, it could still apply since the Wizarding World is the primary setting for most of the series, but it’s an important plot element from time to time that the majority of the planet has no idea magic even exists.
In season 3 of Heroes, Peter is shown a future where a superpower-bestowing serum is readily available to the public.
Though not to superhero levels, Eureka is based on a town where everyone is super intelligent. Zoey was raised outside, so she has had a normal upbringing and lampshades how different the town being this kind of 'super' several times.
In the setting, Gensokyo, even the common humans are capable of magical powers, and are expected to be more powerful than the common fairies. The heroines are simply the ones with either even greater than normal superpowers, or in the case of Marisa Kirisame, someone with normal magical powers who trained and studied really hard to get to where she is.
There's also the interesting case of Sanae, who used to be revered as a god in the outside world and is believed by some fans to have had a hard time adjusting to this trope's effect when she arrived in Gensokyo.
Romancing Sa Ga series game, Sa Ga Frontier 2 had a world where everyone has magic powers as part of their "anima", or life force. It was a major plot point because Gustav, the heir to the throne, mysteriously did not have magic powers, and was banished from the court for his freakish nature. Most of the Romancing Sa Ga series will let pretty much anyone use magic, even if they are not particularly good at it, however.
The Elder Scrolls series (at least, more recent ones) also lets essentially anyone use magic, thanks in part to its very loose class system. In Oblivion, players even start out with a basic attack spell and healing spell before they even get a chance to choose their class, and essentially anyone can just go into a church and get trained in some magic for a fee. Characters who do not use magic simply have chosen to focus on other areas, rather than being incapable of spells.
Many races also start with free skill points in at least one magical discipline and/or supernatural special abilities which require no training, skill, or even magicka (mana). Even Nords, who are typically big brash warrior-types, can call on magical frost once a day and get skill points in Restoration magic. Your birth sign can grant you further powers, including turning invisible.
The denizens of Rapture in BioShock are all addicted to ADAM. Spread across the city are vending machines that turn ADAM into mutations that let you shoot fire from your hands, turn invisible, and control minds. Even the relatively "normal" users of it are much stronger, faster or smarter than an average human.
There supposedly are normal individuals in Paragon City, but aside from the random invincible pedestrian (and maybe the occasional contact) you'll almost never meet them. This is especially true for anyone in the roleplaying community, unless the character in question is powerless as a gimmick.
Kingdom of Loathing It's a very minor part of the setting, but your character will do simple magic - things like lighting your way in dark areas, casting a fireball, etc - in a handful of non-combat adventures even if you aren't a spellcasting class. Perhaps not everyone can do magic, but it certainly seems that all Adventurers can.
In the Star Ocean series most magic users derive their powers from special runes, usually tattooed onto the user. Though more complex ones require training and practice anyone can learn basic spells. Some games represent this in gameplay, with basic attack or support spells as a learnable ability, and others restrict it to the canon magic users.
Suikoden is a similar but even more extreme case of the magic variant. From the strongest warrior, down to the little girl running a card game on your ship, basically everyone can be expected to be armed with Green Rocks of some kind.
Of course, the only reason enemy players would invade a city in the first place would be to kill its ruler, who happens to be a living (or unliving, in Sylvanas Windrunner's case) example of Asskicking Equals Authority.
Pokémon Mystery Dungeon uses this trope. The people with no super powers are from different planets or different time periods and they quickly receive powers when they arrive in the main setting. Even Magikarp can hold it's own here.
Inazuma Eleven, as long as it concerns soccer, even an old hag can create wings if she learns the right skill.
Super Mario Bros. uses this, to an extent. Almost every character, with very few exceptions, has some sort of power. Most of these are apparently species traits, but even the human characters have powers.
As of Halo 4, most of the crew on Infinity are Spartan IVs, even the ones that aren't actively taking part in combat, like Mission Control. The process for becoming one is so streamlined that nearly any marine could volunteer for it.
In Garry s'mod Normally Everyone Has Super Powers They can fly and no longer colide with things they can spawn stuff and other things
The Defenders Of Stan has this as a premise. Everyone in the world except Butt Monkey protagonist Stan has super powers, leaving him as the last human on Earth.
In the Global Guardians PBEM Universe, the villainous Super Robot Omega is from one possible future where the metagene, the source of most metahuman powers, has spread to most of humanity. This has basically left the "norms" (as they are called) an ethnic minority who aren't actually oppressed so much as they are treated by the rest of the population with the same arrogant condescension that Real Life minorities were treated during the days of the White Man's Burden.
In Trinton Chronicles it seems like everybody has some sort of supernatural power, ability, or trait. Some are more powerful than others, but it's so commonplace that if you lack powers, you're more of a freak than if you happen to be born with powers, also magic is a normality and anyone can learn it, like any kind of science, but it takes special people with the drive to do so.
An episode of Darkwing Duck centered on an entire Planet of Superheroes. There was only one "Normal" in the entire population whose job it was to be rescued by the supers. He eventually rebelled and became their supervillain instead.
In Avatar: The Last Airbender, while not everyone is super, in the sense of being able to bend the elements, a large percentage is, maybe around 30 to 60 percent. This means that bending tends to be used not only for cool fight scenes, but to build houses, heat and cool drinks, power steam-punk machines and play games.
Then there are the Air Nomads, who are the most true to the trope. Because of their spirituality, they were all born airbenders.