As of Generation VI, there are over 700 Pokémon in the world, along with thousands of trainers, the anime incarnations of specific mons and characters, and various AU games of Pokémon. When you have this many Loads and Loads of Characters, naturally, some will stand out better than others.
Starter Pokémon and mascot Legendaries (Pokémon that appear on the box-cover) do not apply to this list as they are purposefully designed to be popular and are the closest things to non-human main characters each Generation has. However, that doesn't mean they can't be Breakout Characters.
Spinoff game Pokémon Colosseum has Miror B. Crazy Awesome, literal Disco Dan with a Pokč Ball-shaped afro as the first villain team boss. He never cares about his duties as a boss of a crime syndicate and prefers to practice his dance moves. His Latino-sounding battle theme also contributes to his popularity. In fact, he was so popular that he is the only Cipher member from Colosseum to reappear in the sequel, where you could battle him as often as you want (or until you got all the Shadow Pokémon, whichever came first).
The homeless fat guys◊ that usually hang around starter towns and rave about technology. No seriously, just listen to starter town tunes on Youtube, and count how many times you see someone comment on the fat guy standing there.
In a similar vein, the guys that greet the players in every Gym with "Yo! Champ in the making!" Until the 4th gen... It's unclear if it's a different guy each time or the same one, but either way, he's as beloved as the fat technology guy.
Leaf, the Distaff Counterpart to Red, hasn't appeared in any game besides her debut and is mostly forgotten by Game Freak nowadays but has quite the following. People are always begging for her to cameo or be fightable in games, potentially being a higher level than Red too.
Hilbert and Hilda of Pokémon Black and White are probably the most popular protagonists ever since Red and Leaf due to their overall Bad Ass designs (Hilda being a Tomboy) and the fact that they're teenagers rather than children like the previous playable heroes. Not to mention that Hilda is very frequently shipped with N (see above).
Kris, the very first playable heroine, is not lacking in popularity either, despite only appearing in one game before being replaced by Lyra.
Misty and Brock are this in the games due to their anime and Pokémon Special counterparts. In the games themselves they're just early gym leaders, with Misty having a slightly larger role than most gym leaders in the Johto games. However, thanks to their counterparts, they've become amongst the most popular characters in the franchise.
Similarly, while fans may argue about which generation is the best, there's no denying that Professor Oak is the most iconic and popular Pokémon Professor in the franchise.
In Japan, the Subway Masters Ingo and Emmet from Black and White are ridiculously popular, ranking second and third on a popularity poll despite not having any major role in the story.
They've gotten so popular that they've gotten quite a lot of official merchandise, more than even the protagonists. It's surprising considering they have no real personalities and are barely in the games.
Cynthia, the first female champion from Diamond and Pearl, has also become quite popular. She's managed to appear in HeartGold and SoulSilver and Black and White, which isn't bad considering that Pokémon has non-linear sequels.
Professor Sycamore from Pokémon X and Y has arguably become the most popular professor since Oak, likely due to his design and being the first professor to actually battle you.
As evil teams go, two evil teams are equal to, if perhaps more popular than mainstream evil team Team Rocket, Team Plasma and Cipher. While Plasma is led by several ensemble darkhorses in their own right (N, Ghetsis, ect) and work to question the fundementals of the game itself, Cipher is appreciated for being such an evil team that has no redeeming qualities and played completely seriously as a threat.
Yancy and Curtis from Pokémon Black 2 and White 2. Their main purpose in the games, after a lengthy sidequest is to trade you rare Pokémon with hidden abilities and items. However, they're both pretty popular since they serve as an (Implied) Love Interest for your character. It helps that they're both likeable and pretty cute, especially in Yancy's case.
Riley from Diamond/Pearl/Platinum is also rather popular, at least compared to his fellow "Stat Trainers". It helps that he's a major Bishōnen.
Pokémon - Generation I
Cubone and its evolution Marowak are remembered partially because of their interesting design, use of bones as clubs, tearjerking backstory, and the fact that they're the only Pokémon in G1 to have actual story relevance (the next closest to having to do with the plot was Snorlax, who simply was a Broken Bridge).
Pidgey. Still liked by many fans despite its shortcomings for being the original Com Mon bird. Perhaps it's the fact that it may have been the very first Pokémon to actually be caught by the first Pokémon trainers, or simply because it's cute.
Add to that the fact that it evolves into the badass-looking Pidgeotto, which was also heavily featured in the anime early on. Its final evolution, Pidgeot, is also not actually a bad Pokemon in the endgame.
Similarly, Ratatta is liked due to the top percentage meme mentioned above, and the fact that it's also the center of the "FEAR" strategy.
Meowth, probably because of its appearance in the anime. Almost the same case as Pikachu, but toned down quite a bit.
Vulpix/Ninetales. You don't have to go far to see the MANY fan-fics that claim this to be Naruto's favorite Pokémon. Add in the fact that the fox Pokémon were given Groudon's Drought ability, bringing about its usage in Sunlight teams.
Koffing is fairly popular for being a Perpetual Smiler. While there are several others in this series, what puts Koffing above the others is its theme of smoke, causing many to interpret it as stoned. Its status as Smogon's mascot is further testament to its popularity. Weezing, despite its depressing face, still has its fans as a Mighty Glacier whose Levitate ability allows it to No Sell the more threatening of its two weaknesses.
Gengar has always been considered one of the more powerful and cool looking ghost-types. In Gen I, it was the only fully evolved Ghost type. Even with the introduction of other ghosts, it has always managed to remain in the higher tiers, and is the only Pokémon to be in Smogon's OU tier in every generation. Its Mega Evolution is no joke either due to its ability becoming Shadow Tag, and is also considered better than most Legendaries.
Its pre-evolution Haunter is quite popular as well, often considered more visually threatening.
Magnemite gained in popularity over the years. First, becoming a steel-type in the second generation, which greatly increased its usability. Then, it gained a secondary evolution in Generation IV which made it a powerful Steel-type special user. In Pokémon Black 2 and White 2, Magnemite were used in the Magnemite Coil, a form of Emergent Gameplay, in Join Avenue. note An area in the game lets you set up shops where you get services not offered elsewhere, like leveling up your Pokémon, buying berries, or buying common items cheap in bulk to sell at higher prices in other stores. If you trade Pokémon with other people, NPC's modeled on these trainers will arrive at the area and interacting with them will either let you set up the shops you want or "level up" the already existing shops, thus expanding their services. Cue Magnemite: being one of the earliest Pokémon available in the game, if you catch one and go to the Global Trading Station at any Pokémon Center, you can trade Magnemites of any kind with trainers from all around the world. This way, you can get more NPC's to level up your stores and use their services much sooner than you would otherwise.
Pinsir was another well-liked Bug Pokémon from the first generation, but lost a lot of support over the years due to being overshadowed by the likes of Scyther (Scizor), Heracross, and Scolipede. Generation VI, however, finally throws Pinsir a bone and bestows upon it a Mega Evolution, putting Pinsir back on the map for the fan-base.
Slowbro got nicknamed as "Funbro" in Generation VI thanks to the discovery that he can obtain a move-set that would force players to be stuck in a never-ending battle. Slowbro is now basically considered to be the king of trolls in the Pokémon world.
Starmie. A (mostly) unique dual-typing and incredible stat distribution / move-pool has Starmie in Smogon's OU Tier up until Gen VI; being able to pull off any role that the player wishes for.
Before it gained an evolution, Chansey was greatly appreciated for being the only Pokémon that could actually stand a chance against Mewtwo (besides fighting it with another Mewtwo) due to it's high HP stat. And even after it's evolution was introduced, Chansey would later receive a gift from the gods in the form of the Evolite item which skyrockets its defensive stats to levels Blissey could only ever dream of having; giving competitive players a tough choice as to whether evolving Chansey is worth it or not.
Eevee simply for being the reason Eeveelution exists.
Jolteon for being one of the few Pokémon that could take down Psychic types in the first generation due to its blazing speed. Competitively, it has the honor for always being in the Overused tier prior to Gen VI.
Flareon gained quite a following other the years mostly for being the underdog of the Eeveelutions; getting constantly screwed over for never receiving any moves to take advantage of its monstrous attack stat until Generation VI. And even then...it still suffers a lot of problems.
Vaporeon as a highly competent Bulky Water competitive use Pokémon.
Ditto has always been considered the ultimate pimp of the Pokémon universe due to its nature of being able to breed with any other Pokémon that can breed. In addition, its popularity drastically increased after it gained the Impostor ability from the Dreamworld in Generation V; buffing the pink-blob from a useless gimmick, to one of the best revenge killers in the game.
Dragonite, Generation I's Pseudo-Legendary and the only Dragon-Type at the time. Dragonite waned in popularity as the generations went on due to being overshadowed by Salamence and Garchomp, but once Generation V bestowed upon it the hidden ability, Multiscale, its usability skyrocketed.
MissingNo, in a mixture of Good Bad Bugs and Memetic Mutation. The fact that his presence glitches the world in a hilarious manner and replicates the item in the 6th slot (useful for Master Balls and the like) helps a lot, too.
Mew, the kitten-like predecessor to Mewtwo, is popular due to its rarity (being an event-only Pokémon, unless glitches are used), cuteness, and overall versatility, as it can learn every single move that can be taught with an item in the game.
Mewtwo is never left out whenever the subject of legendaries comes up.
The baby Kangaskhan holds has a large popularity. If someone is creating their own fan generation and Pokémon, the baby is a popular choice for a Pokémon. IT got a Mega evolution and not its mother, which is by far the most powerful of all the megas.
Heracross retains a high level of popularity, partially due to Ash's Heracross, and partially due to its unique typing and good stats. It even got a Mega Evolution. This is in spite of the fact that in Gen. II it was not only hard to find, but also pretty useless with a very weak movepool and almost no STAB moves. It may also have something to do with the face that Rhinoceros Beetles are popular in Japan and Beetle Fighting is a popular pastime.
Scizor. An evolution to a Pokémon that was already a Darkhorse. Gains a Steel-Typing and new design to make it even more Badass, and then gains an ability a few generations later that makes its Bullet Punch one of the most feared attacks in the game, even in Ubers.
Forretress. Created specifically to Stone Wall the Normal-Type kings from Generation I, and the only Pokémon that can set up all entry hazards (before Gen VI introduced Sticky Web, which it didn't get).
Quagsire. While not particularly great in-game or stat-wise, Quagsire's laid back nature and goofy smile has made him a mainstay in forum/imageboard threads about pokemon best suited to being a "bro". It got so popular on one board that it became its mascot, and is featured in most of the banners concerning said board.
Nobody is quite sure why Dunsparce is as popular as it is, yet people demand that it gain an evolution.
Pokémon - Generation III
Ludicolo has been one ever since it was solidified as Miror B.'s (a Darkhorse in his own right) signature Pokémon.
Aggron, who restores mountains and looks like an even more Badass metal version of another Darkhorse, Tyranitar. The fact the Aron and Larvitar lines are version exclusive counterparts for the Generation VI games furthers this connection that people make towards Aggron.
Gardevoir is a Rule 34 magnet and would often place high in popularity polls and even got a Mega Evolution.
Flygon; its unique typing and design stood out amongst all other Dragon Pokémon...at least before the Gible line was created. This, however, did not diminish its popularity; a dedicated and strong fan following still prefers to use it over Garchomp. It's still useful as a scout that's immune to Earthquake (something Garchomp does not have) and entry hazards like Spikes and Toxic Spikes, and its design is still considered quite unique.
Although rarely used in competition, Mawile is adorable and popular enough to be given a Mega Evolution.
Metagross, the only Pseudo-Legendary that's not Dragon-like and from the only generation to release more than one Pseudo-Legendary. Its duel Steel/Psychic typing is also quite a god-send in competitive play; rivaled only by Bronzong which was introduced in the next generation.
Starly, a Com Mon similar to Pidgey who quickly becomes a Disc One Nuke. It learns great moves like Wing Attack early on, and eventually evolves into the Big Badass Bird of Prey Staraptor, one of the rare Flying-Types capable of learning Close Combat. In fact, many have considered it one of the best Pokémon for completing the main story, period.
Glaceon. It's like an Ice-type Espeon, except that it's a LITERAL Mighty Glacier.
Its counterpart, the long awaited Leafeon, isn't that far behind in popularity.
Hippowdon use caught on post-Generation IV with the many additions made in Generation V; increasing the utility of using Sand teams to take advantage of Hippowdon's ability to summon instant Sandstorms. Unlike Tyranitar (who also gets Sand Stream), it has Slack Off, much more physical bulk, and FAR fewer weaknesses (3 as opposed to Tyranitar's 7), making it a very good wall.
Abomasnow is often overlooked, but has its own loyal fanbase following amongst competitive players; particularly for being the staple of Hail teams as the only Pokémon that can summon instant Hail. Its typing sure doesn't do it any favors; having seven weaknesses turns many players away at first glance. However, it turns out that the weaknesses consist primarily of the lesser-used offensive types in competitive play, such as Poison, Steel, and Bug, and that the resistances Abomasnow does have are actually quite useful in competitive play; Water, Electric, and Ground specifically. The fact Abomasnow was one of the few Generation IV Pokémon to receive a Mega Evolution is no coincidence. On a side note, it's also quite prone to Barack Obamasnow jokes.
Garchomp, Generation IV's Pseudo-Legendary. Particularly popular with the older crowd because of its incredible power, and popular with the younger crowd because it resembles what you'd get if you combined a Dragon, a shark, and a jet-engine fighter plane. It's also famous for being one of the first non-Legendary Pokémon to be banned by Smogon.
Darkrai is immensely popular for its design, battle style, and two WIDELY different depictions (The Movie Darkrai and the Mystery Dungeon Darkrai have virtually no similarities).
Deerling gained quite a following over the years for changing colors, being cute, being a deer, being a grass type, holding its own in battle, and for having an awesome evolution.
A LOT of fans wish Joltik was the most well-known Electric-type.
Excadrill, one of the most annoyingly powerful non-legendary Pokémon you'll ever fight against. Their existence (along with Garchomp) are the reason sand teams became such a threat in the Generation V meta-game.
Scrafty is also a very well-liked Pokémon from Generation V. It looks cool, has an interesting theme, and is uniquely useful in competitive play; it and Scraggy (its previous form) are the only dark/fighting types, which means they're the only fighting type Pokémon immune to psychic attacks note Well, at least before Generation VI's Pangoro came along, which is fighting/dark and, therefore, shares similar immunities and weaknesses, and they get STAB on two very useful types. Scrafty's possible abilities are also very good. Moxie increases its attack every time it defeats an enemy, making it a good sweeper. Shed Skin has a chance of removing a status effect, so it's great for a defensive set. The official Nintendo 2011 Black and White tournament gave out a fairly decent Scrafty as a nod to its popularity as a team fighter. It likely helps that Scrafty is really useful in-game as well, with its typing rendering it good against three of the Elite Four.
Chandelure. Right up there with Gengar as one of the best Ghost types of the game thanks to its god-like special-attack and amazing type coverage. Which is ironic considering the status most other Pokémon based on inanimate objects get.
Volcarona and its pre-evolution Larvesta. Thanks to it being an excellent Pokemon battle-wise, possessing a unique type combination (Bug/Fire), and for being a fluffy moth.
Golurk is a freaking Humongous Mecha! The moment people figure out it can learn Fly ups anyone's view of the giant robot. Also has the unique typing of Ghost/Ground.
Hydreigon, Generation V's pseudo-legendary and the signature 'mon of the aforementioned Ghetsis.
Genesect, a prehistoric insect-turned-cyborg weapon of mass destruction. Based on the trailer for the next movie, a Transformer too. This only served to increase its popularity.
Pokémon - Generation VI
The Kalos bird, Talonflame, picked up a fanbase on the competitive side of things the moment people realized just how good its signature Hidden Ability, Gale Wings, is; giving it +1 priority to all Flying-Type attacks, including Brave Bird, Tailwind and Roost.
Skiddo and Gogoat. Both can be ridden on in game. Skiddo is a cute little goat kid, while Gogoat is cross between an adult goat and a motorcycle with good stats and a surprisingly large movepool when compared to other Grass-types.
Espurr and Meowstic, the Creepy Cute cats. Especially Espurr, whose Thousand-Yard Stare quickly achieved meme status and recently had a whole range of merchandise revolving around it released.
Despite a rough start regarding Honedge and Doublade's shallow designs, the possessed sword's final evolution, Aegislash more than made up for it with an Awesome McCoolname in every language, a cool semi-humanoid design, and great viability in competitive play; giving the Pokemon swords as-a-whole a much better reception amongst the fans.
The sauropod Ice fossils Amaura and Aurorus didn't go unappreciated, either. You'd be lucky to come across a Pokémon forum that hasn't made a The Land Before Time or Jurassic Park joke with the new Poké-dinos.
Pumpkaboo and Gourgeist, one of two new Ghost/Grass type families introduced this generation clearly saw more popularity than the Phantump/Trevenant line for their adorable, unique, and creative design (Halloween and pumpkins) and for coming in four different and unique sizes ranging from small to super size which isn't simply a cosmetic difference, but also are seperated from one another from how one uses them (small tends to be speedy sub-seeders whilst the Super-Size are very bulky).
In general, Game Freak claims that on of the main factors behind who received Mega Evolutions was popularity.
Mega Kangaskhan is popular due to its ability, Parental Bond, allowing most moves to hit twice.
Mega Mewtwo X. The smaller, less menacing and much more widely-marketed Mega Mewtwo Y got a mixed reception from fans, with its portrayal in the divisive 16th anime movie not helping matters. Then, Mega Mewtwo X was revealed, and fans adored it for its tougher and more masculine design, despite only getting a tiny percentage of its Y counterpart's publicity even to this day.note While Mewtwo itself is a heavily-publicized character already known to be very popular, Mega Mewtwo X was not, especially compared to Y.
Mega Garchomp is considered to be a huge darkhorse amongst all the other Mega-evolutions (with the exception of Mega Kangaskhan). The reason being that while all Mega-evolutions are usually just significant stat-buffs, Garchomp's Mega-evolution actually has a completely different play-style compared to its normal form; allowing for Garchomp to utilize Rock and Steel-type moves over its normal move-setsnote :Steel being IMMENSELY helpful for a generation that introduced the Fairy-type as it gives Garchomp a means to fight back thanks to the Sand Force ability Garchomp switches to in its Mega-evolution.
Misty has not been a main character on the anime since 2003, yet she's still popular among the fanbase, even among viewers who started watching years after she left the show.
Some of the Characters of the Day get this as well. Gligarman (an obvious Batman and superhero parody) was popular enough to frequently get requested to return to the show, especially when Ash had a Gligar/Gliscor of his own.
Conway, an intended one-shot who was added to two other story arcs (the Pokémon Summer Academy and the Sinnoh League) due to fan popularity.
Pokémon Hunter J, for really pushingthe envelope in terms of how dark the anime can get. She is a No-Nonsense Nemesis and also one of the very few villains who actually tries to murder Ash as opposed to just getting rid of him.
Harley, because he's such a Jerkass and yet sodamnFUNNY at the same time. He was also the first genuinely antagonistic rival in the series who remained an antagonist and not change his behavior, which the fans greatly appreciated.
Ursula, a one-shot character of the day that becomes a full-fledged rival for Dawn in the next season due to fan popularity for being an antagonistic rival; separating her from Zoey, Kenny, and Nando.
Amongst Ash's numerous rivals, Stephan has become one of these. Being less prominent than Trip or Bianca (among others), he nonetheless has a lively and likeable personality, as well as being a Badass battler from what we get to see of his skills. It also helps that he gets what is, hands down, the best battle in the entire Unova League.
The Club Tournament contestants - many don't even get any lines, but their character designs are regarded as among the best parts of those arcs (Antonio and Jimmy Ray/Watchog Guy especially). Some of these characters, like the aforementioned Antonio, return for the Unova League.
Edmund the "Rain Man", who's an (almost literal) One-Scene Wonder (he appears momentarily before battling Stephan, and disappears altogether afterwards).
Despite only appearing in one game and a single episode, Lucy the Frontier Brain is very popular and one of the main characters shipped with Brock.
Similar to the above Lucy example, several girls are this for shippings with Ash despite not being one of his primary traveling companions.
Bianca from Pokémon Heroes for, again, cheek kissing Ash at the end of the movie. (Though, if this was actually Latias has always been up for debate)
Frontier Brain, Anabel, maintains a fanbase for Abilityshipping
Angie, a tomboy from the Sinnoh Summer Academy arc for Morpheusshipping.
Several of Ash's Pokémon have developed rather large Fandoms over the course of the series due to their sheer Badassery or quirky personalities. The most notable being Charizard, Heracross, Swellow, Sceptile, and Staraptor. Even Ash's unofficial Pokémon, Haunter and Larvitar, have a place in fans' hearts.
Psyduck and Wobbuffet, two very similar, dopey Pokémon who just won't stay in their Poké Balls.
Ash's Gliscor. What wins a lot of people over towards this Pokemon was how utterly cute the anime made the flying scorpion out to be despite its supposed god-awful design.note A vast majority of people thought Gliscor's design sucked when they first saw it. If any Pokemon ended up getting a better reception compared to when they were introduced in the game beforehand, it's this one.
Ash's Gible. There's just something about it's blank, wide-eyed, personality that draws people to adore the tiny land-shark. Also helped by the fact that its capture was Ash's first legitimate pseudo-legendary Pokemon.
The Ducklett trio from an early Best Wishes episode, who caused bizarre, yet adorable chaos and trolled the characters several times. Ask any Pokémon forum about them, and you'll see they're almost universally loved.