Gao Gai Gar: Guy Shishio and his girlfriend Mikoto are transformed at the finale of the series into Evoluders, which is stated as the pinnacle of human evolution. As shown by Guy in the later OVAs, Evoluders are able to run as fast as a bullet train, are incredibly strong, can fly, and can survive in the vacuum of space thanks to a nifty green aura they can generate.
Mobile Suit Gundam: Newtypes were originally written as the next stage of human evolution, but later series distance themselves from this concept. The finale of Gundam X explicitly debunks the notion; it is, however, set in an alternate universe to the majority of the series featuring newtypes, and doesn't use the term "newtype" in the same fashion as them, so whether this holds for the other series or not is questionable.
This trope is humorously subverted in Mobile Suit Crossbone Gundam: when several people that believed rather heavily in newtypes being the next stage of human evolution are shown newtype monkeys, they don't take it well.
not the Innovades, who rather confusingly called themselves Innovators during the second season, the bunch of people that possess psychic powers (as much as any other gundam series)
appear to play the trope straight, with the minor difference that the "evolution" was not entirely natural: it requires the person to be exposed to GN Particles, which do not occur naturally on Earth. By the series' Distant Finale, set 50 years after the conclusion, it is stated that fully 25% of humanity have become Innovators, with the implication that eventually the entire human race will have metamorphosed.
Mobile Suit Gundam AGE: The X-Rounders are said to be an inversion of the concept. Rather than being more advanced, their powers come from tapping into more bestial, instinctive areas of the brain that modern humans no longer use.
Black Jack: A mid 90s movie featured groups of people who had developed incredible and highly advanced abilities in a variety of fields, including athletics and art, used the "next stage" terminology. They developed extremely dangerous side-effects also, and it was eventually revealed that, apparently, limited exposure to chemicals found only in a remote desert migrated across the world and advanced certain individuals by accentuating their natural and pre-existing talents.
Devilman Lady by Go Nagai: The reasoning behind humans suddenly transforming into monsters in the anime adaptation is that they are flukes in the first stages of humanity's next evolution and based on the transformee's talents and personality (e.g. a talented swimmer grows gills and scales, someone with severe A God Am I might become an angel, etc.) The main character is a frail young model that represses all ' inappropriate' feelings, thoughts, and urges. She transforms into a violent, muscular demon with no inhibitions.
Hunter × Hunter: The chimera ant queen transfers the "most worthy" DNA of whatever she eats to her progeny, resulting in every batch of eggs giving more powerful (and human-like, since humans are the best food) ants than the last, culminating in the King being the supreme being.
Getter Robo: A major theme, since the energy that powers their Humongous Mecha is the spirit of evolution itself, or taken another way, the embodiment of life/survival itself.
Elfen Lied: The Diclonius. Well, probably. Maybe. The conspicuously nameless government agency claims they're our evolutionary superiors, genetically programmed to take over the earth in cold-hearted genocide. The protagonists quickly find out that, at least, they're not cold-hearted at all.
One of the ideas in Stardust Memories is that evolutionary levels are contagious on a mass scale—if a world has primitive life, and it's visited by humans, that primitive life will rapidly evolve to fill all evolutionary niches required in order to produce human-like creatures. Unfortunately, it may hit an evolutionary dead end during the attempt . . .
X-Men All mutants comics dub mutants "homo superior", the "next step" in human evolution. A long-established but seldom-mentioned trait of Marvel's mutants is that they're a little tougher than a normal human of the same frame. E.g., In her solo comic, Dazzler mentions that one of the advantages of being a mutant is that she doesn't get tired as quickly as normal people, and the old Marvel-based Role-Playing Game gave all mutants + 1 level in the Endurance stat.
Mr. Immortal, who is so evolved that he's not just "homo superior", he's "homo supreme".
Excalibur: One issue (written by Chris Claremont) says that all mutants are just a bit more in every department. Nightcrawler, for example, healed from his broken leg a bit faster then a regular human would. Nightcrawler doesn't have healing powers, he's just That Awesome because he is a mutant.
Sometimes, Galactus is said to target worlds at the "apex of their evolution" to devour. For evolution to have an "apex", it has to be a finite process with multiple levels, and a highest, "best" level.
The Kree, one of their subplots involved them being "unable to evolve" and needing Half-Kree Hybrids to further their "evolution", suddenly turning the whole race into the "self-evolving" Ruul.
DCComics' Captain Comet is supposed to be the next stage of human evolution ("born a hundred thousand years before his time!") In the New 52, his "species" is called Neo Sapiens.
DC Comics also has a villain named the Ultra-Humanite, whose very name suggests this trope. Unusually for an "advanced human", he's not physically frail at all. Rather, he combines Super Intelligence with Super Strength, as he has a superhumanly intelligent genius' brain in the body of a super-strong white gorilla. However, he had his brain transferred into that body, so he's closer to Grand Theft Me than Perfect Life Form.
X-Men: In the movies, despite insistence from Magneto that they are "homo superior," it's established that mutant powers are actually a result from a simple genetic carrier, "the mutant gene".
Evolution: The aliens started out evolving to fit the ecological niches they found themselves in, but were eventually shown as evolving along a fixed path, becoming dinosaur-like things and then primates for no reason. In addition, despite the rapid evolution that was the point of the film, there was no sense that the creatures were going through multiple generations particularly rapidly. (There was also a cartoon series based on the movie that made the same mistakes, only more so.) One interesting aversion, however, is that the final form achieved by the creatures when forced through rapid evolution was essentially a giant amoeba. It's explained that this is the most efficient form for its particular environment so it can be considered the best adapted even though it's one of the simplest.
Creature from the Black Lagoon: The titular creature as "the missing link" between man and fish, being a clawed, super strong, bipedal amphibious dinosaur from the Paleozoic. In the third movie they even try to "evolve" him into near human, and educate him. This ends badly.
Super Mario Bros.: The entire plot is based on the idea of evolutionary levels. The brothers stumble on another dimension in which humans exist, but they evolved from dinosaurs instead of apes. When hit with a "de-evolution" gun, humans from our world turn into chimpanzees and the humans of the alternate world turn in to large, human-like dinosaurs. The rightful king of the other realm had been "de-evolved" into a fungus and is re-evolved into a human at the end. Also, Koopa uses a machine to "evolve" Spike and Iggy, which makes them extremely intelligent.
(George does something stupid) Ape: And they say humans are "more evolved".
Literature
She by H Rider Haggard: The climax has the title character take another bath in the life-giving flame, which takes away her youth. Her dying form is described as being like a monkey. Darwin's theories had only recently entered the public consciousness when the book was written and the whole story is about the fear of "devolving" since people were scared that it might work backwards at the time.
Odd John by Olaf Stapledon: The titular character is one of a new species of supermen who happen to be born here and there around the world at roughly the same time. This story is apparently the origin of the term "Homo Superior" for such beings.
Last And First Men by Olaf Stapledon: After leaving a dying Earth and settling on Venus, humanity goes through eighteen stages of evolution, each adapting to their unique environment. For example, the dwarf "Ninth Men" who are limited by size due to excessive gravitation, the flying "Sixth Men" who live a harsh existence competing their seal-like relatives, and the "Tenth to Seventeenth Men" whose sentience reemerges after the "Sixth Men" civilization crumbles into savagery.
"The Man Who Evolved": The whole premise of Edmond Hamilton's 1931 short story. In the story, a man uses a modified form of radiation to evolve himself in minutes. In the end, he eventually evolves into protoplasm, since, for some reason, evolutionary levels apparently go in a cycle.
Hamilton liked the idea that radiation caused evolution, since he took the implication to be that worlds without radioactive elements would have little to no evolution. "Devolution" takes another approach to the same problem: the highest form of life to ever exist is a kind of alien bacteria that forms a benevolent Hive Mind. All life on Earth is descended from some of that bacteria that was stranded here, but evolution has weakened rather than strengthened us, costing us our unity.
Among the forest-covered hills of the northwest exist wandering bands of ape-men, without human speech, or the knowledge of fire or the use of implements. They are the descendants of the Atlanteans, sunk back into the squalling chaos of jungle-bestiality from which ages ago their ancestors so laboriously crawled. To the southwest dwell scattered clans of degraded, cave-dwelling savages, whose speech is of the most primitive form, yet who still retain the name of Picts, which has come to mean merely a term designating men — themselves, to distinguish them from the true beasts with which they contend for life and food. It is their only link with their former stage.
Arthur C. Clarke's Childhoods End: The book is fundamentally about most of humanity evolving beyond their corporeal forms into a mass consciousness and merging with a universal psychic gestalt. (If this sounds familiar to anime fans, Hideaki Anno has cited the novel as a major inspiration for Neon Genesis Evangelion.) The story also features the Overlords, alien creatures that are an evolutionary cul-de-sac of sorts, who are apparently unable to achieve this level of evolution for some reason.
2001: A Space Odyssey: The series discusses the "evolution" of the Sufficiently Advanced Aliens who brought The Monolith to Earth. Read literally, it's an example of this trope, but is actually a case of a species reaching a point technologically where they can perform Brain Uploading into machine bodies and then finally turn themselves into Energy Beings — self-directed evolution rather than natural.
In The War Against The Chtorr, it's stated that since Chtorran lifeforms have a billion-year evolutionary head start they have a massive advantage over Earth lifeforms.
Discworld: The God of Evolution's personal project, the creature he's been working to perfect for centuries: the cockroach.
Another Discworld example: In Carpe Jugulum, Lord Magpyr refers to fairies and Igor as evolutionary cul-de-sacs, although he was probably just being arrogant and mean, rather than making any thoughtful judgments on their place in the world.
Parodied in Tomorrow Town by Kim Newman: one of the claims made by the futurists who have set up shop in Tomorrow Town is that they have evolved beyond their 1970s contemporaries, or 'yesterday men' as they are called. Like most things to do with their "futopia", they're quite, quite mistaken.
One theory for the Weaver race's origins, as mentioned in Perdido Street Station, is that normal spiders were subjected to occult forces that bumped them up several Evolutionary Levels, from mindless bug-eaters to something akin to an Ultimate Life Form.
In Edgar Rice Burroughs's Caspak trilogy each individual begins as tadpole like creatures and slowly evolves over its lifetime until it reaches its proper niche where it stops. The one exception are the humans at the peak of this ladder, some of whom have reproduced the normal way.
Live Action TV
Time Trax: Humanity is depicted as being on the cusp of an evolutionary advance granting some (almost realistically) minor abilities such as greatly enhanced agility and the ability to "time stall" (Nothing strange and extratemporal: the term refers to an ability to alter the way the brain processes sensory data giving the perception of time slowing down). An episode featured protagonist Darien Lambert meeting a young boy with enhanced athletic skills similar to what's described above. Darien wondered if this boy might be the "missing link" between the present humanity and future humanity. In the end, it turns out the boy is himself from the future, brought there by his father when he was very young.
Star Trek: Evolution may indeed work differently in the Star Trek Universe thanks to Ancient humanoids. Spock explains:
"The actual theory is that all lifeforms evolved from the lower levels to the more advanced stages."
The Next Generation episode "Genesis" had the crew "devolve" thanks to a "de-evolutionary virus". In addition to having the crew devolve to specific "levels", the Earth-species had their levels completely wrong. Riker turned into a neanderthal-like creature (they split off from the human evolutionary tree), Picard begins turning into what Data suggests is some kind of lemur-like creature (which split off from monkeys/apes entirely) and Barclay turned into some sort of spider-thing (Which is...wait, do we even need to state how fundamentally wrong that is?). What takes the cake is what poor Spot turns into. She ends up turning into an iguana which then somehow manages to give birth to kittens.
The Tomorrow People: The entire premise revolved around "the next step in human evolution".
Heroes: The voiceovers at the start and end talk a lot about how the next stage of evolution comes about.
Jekyll: The nasty team of goons after Dr. Jackman want him because he is "the next stage in human evolution". In this case, it is implied that the original Jekyll had hundreds of kids, becoming responsible for many, if not all cases of identical twins and so forth.
Stargate SG-1: All sentient species apparently evolve "towards" ascension. The level right before evolutionary ascension, people will have all kinds of Psychic Powers, such as mind-reading, telepathy, healing powers and some kind of super-intelligence.
In Kamen Rider 555], the Orphenochs consider themselves "the next evolution of man and animal." The reason most Orphenoch victims turn to dust instead of new Orphenochs (their killing method and siring method are one and the same) is because most humans cannot survive such "rapid evolution." Pity full Orphenochs will actually not survive much longer; finding the Orphenoch King is the ultimate goal because only he can 'complete their evolution' and fix the greatly reduced lifespan an Orphenoch will otherwise have, at the cost of the Orphenoch's ability to resume human form. However, since the 'next evolution' thing is something only the villains' organization says, as opposed to a scientist character saying it in all seriousness, it may just be the bad guys thinking highly of themselves rather than writers who need to look up 'evolution' in a dictionary.
Tabletop Games
Magic: The Gathering: The Slivers seem to be an insectile species that have evolved the ability to evolve faster and share genetics through some sort of psionic link, resulting in not just momentary changes to genotype but also phenotype when two different varieties are in proximity. In addition, some flavor text references Evolutionary Levels. The Ghostflame Sliver, for example, seems to be a reference to the common misunderstanding of the punctuated equilibrium theory, as they are "on the cusp of evolution", but it's most notable in the Sliver Overlord, which declares it the end of evolution. Then again, the Slivers evolve so quickly partially by devouring other life forms and adapting their advantageous genes to their offspring, grow rapidly to adulthood, are semi-sentient, act in concert, and are almost virus-like in their ability to infest, consume, and spread rapidly, so it might just be an intimation that the Slivers will kill everything on the planet, halting evolution permanently.
Marvel Superheroes Role-Playing Game: Among the list of powers available to players, some sort of "Hyper-Evolution" power that lets a hero shift up and down along their "evolutionary path," generally affording them the ability to "devolve" into cave-man form (temporarily lower their intelligence to raise their strength) or "evolve" into frail but hyper-intelligent (and possibly psionic) "future" form. The write-up for the "Evolution" power in MSH even lampshades it: "This is comic book evolution, people, the kind where super-strong cavemen eventually evolve into giant brains with vestigial limbs."
Mutants And Masterminds took it a step further with their version of the "super-evolution" power, with five "phases": a barely sapient mass of corrosive protoplasm, a strong feral caveman, a modern day human, a physically atrophied big headed genius, and a being of pure psychic energy. Suggestions are also given of putting dinosaurs somewhere in the middle, revealing exactly how serious the whole idea is, which is absolutely not.
Played With in the Forgotten Realms game Pages from the Mages: The spell "Evolve" changes a normal animal into an intelligent and more or less human-like form. The punchline is that glorified name aside, the spell just permanently transforms the target halfway to its caster (presumed to be a human smart enough to use a 8-level spell), using his own blood sample(!) as a component.
Warhammer 40000: The Tyranids avert this. While they "evolve" at a hyper-accelerated rate (accomplished by devouring entire biospheres, then using the material to spawn custom-creatures) most of these creatures are short-lived, and allow their superiors to devour them once they've served their purpose. It's bizarre and science-fictiony, but the sheer fact that it's portrayed as being generational makes it closer to Real Life evolution than most of the examples on this page.
Video Games
Command And Conquer: Kane believes Tiberium holds the key to the next stage of human evolution. However, this is closer to actual evolution; rather than just being more powerful, the Tiberium mutants in the series are more capable of surviving in the Tiberium-infested regions of the world (about 90% of it). Strangely, Nod still considers the mutants abominations.
EVO Search For Eden: In each chapter, you start as a "basic" version of whatever the chapter is about (fish, amphibian, reptile, mammal), and you gain "evo points" by eating other animals, which you can then turn in to alter your body parts. Oh, and whenever you evolve a body part, you get the helpful message "MYSTERIOUS TIME STREAM EVOLVES YOU." Also, occasionally (say, when you're a reptile or mammal and have to do a water stage), you'll get the message "CHANGE IN CIRCUMSTANCES CAUSES EVOLUTION", followed by your character's feet becoming fins. Even if you're a mammal, or a bird.
Super Robot Wars: Alfimi was created to be the "apex of human evolution".
Mass Effect 3: the Catalyst claims that merging all organic and synthetic life is the 'next step in organic evolution'.
Western Animation
The Simpsons: An overly longcouch gag sequence features the evolution of Homer. This starts with single-celled organisms, then goes from jellyfish to fish to lizard, rodent, monkey, ape... and finally to the modern Homo sapiens before showcasing several historical eras ending in modern Homer walking into his house. This showcases the supposed evolutionary levels misconception. And subverted for Rule of Funny; he meets Moe on the way who walks in the opposite direction... and devolves.
The characters find the lost city of Atlanta, in which the human inhabitants have evolved into mermaids. When Bender points out that this should have taken millions of years, the mayor's daughter explains that the caffeine from the Coca-Cola bottling plant sped things up.
After being Un-Canceled, the Professor accidentally creates evolving robots, who evolve much faster than organisms. Within a few days, they go from microscopic plankton-esque lifeforms to murderous trilobites to dinosaurs to cavemen to modern humans to Energy Beings.
Earthworm Jim: This was Bob the Goldfish's schtick. He tried various schemes to evolve himself into a higher form of life, in one instance using a contraption that stole "Evolutionary Energy" from other creatures, turning people into apes & Princess Whatshername into a ladybug & such. He evolved from a goldfish... into a goldfish. Despite the fact that Bob himself had claimed evolutionary superiority before, he was very unhappy with this outcome.
In Ben 10 Ultimate Alien, the Ultimate forms are from the Ultimatrix's "Evolution" function which the Omnitrix lacked. All There in the Manual explained that the Ultimate forms are computer simulations of what the species would be like after millions of years of having to survive a programmed worst-case scenario. The actual DNA the Ultimatrix uses is temporarily changed to match the simulated DNA.
The Transformers are said to have slowly evolved over the eons (as stated in part two of Desertion of the Dinobots). Apparently Giant Robots can do that.
