Dawn and Zoey's relationship is just tinged with romantic subtext, to the point in Zoey's first Japanese appearance many fans on a certain forum made jokes about her and Dawn.
It doesn't help how hard Dawn took Zoey's words to heart.
Even before Zoey appeared in an episode, the pairing had tons of fans.
One could also argue that Giovanni is the center of a Love Triangle with Meowth and Persian. Meowth's Boss fantasies sometimes make Giovanni go chibi and other times make him very musclebound. But typically Meowth's ultimate goal seems to be just being petted by Giovanni.
Then there's Ash and Gary once it stops being Foe Yay.
Morty spends nearly all of For Ho-Oh the Bells Toll withdrawn and sullen. Bear in mind that in previous episodes he was outgoing and happy. The target of his attitude switch is his friend Eusine, who's shown up with a Suicune fixation and a bad temper, leading many in the fandom to believe that the two have an unresolved past relationship. Also bear in mind that Eusine's subsequent Legend of Thunder appearance has him in turn being upbeat and caring, so it may be a two-way street.
Brock and Ash have their fair share as well. Particularly in the episode "Two Degrees of Separation" where in one instance Brock introduces Ash to a female driver named Claudina who he'd been hoping to score with. Interesting to note that in the entire time he's doing so he's being all touchy feely with Ash, hugging him close and poking and prodding at his face in a playful manner. Later, he finds out that Claudina already has a boyfriend and she drives away. Which leads to this scene from the English dubbed version.
In the episode Love at First Flight May tricked Ash into dressing up as a woman they had just met, named Juliet, in order to help a man named Romeo confess the feelings that he had for Juliet. Brock tried to help out too and ended up getting carried away, even chasing poor Ash around and trying to hug him while declaring "My sweet Juliet! Heal me with your love!" * releases hearts*
There's also a bit of this between Pikachu and Meowth, doubling as Foe Yay. One of the Japanese endings (which was sung by Meowth's seyiuu) even featured the two dancing together. note A rather humorous bit of trivia regarding this pairing—Meowth and Pikachu are part of the same egg group, meaning that if one of them was female, they'd be capable of breeding!
This scene, where Seymour hugs Ash for saving him.
Misty's excitement over meeting her water Pokémon idol, Prima, seems at times to be rather focused on Prima's chest.
When N showed up in Best Wishes, fandom speculated there'd be some of this between N and Ash. (Never mind N is a lot older and Ash is 10.)... seems like◊ the shippers◊ were right◊.
The B&W episode All For The Love of Meloetta brought back Cynthia. When Ash talks to her, he and Cilan act as they usually do while Iris stares vacantly at her. When Cynthia does try to talk to her, Iris outright blushes and twiddles her fingers as if she were talking to someone she had a major crush on. Cynthia's outfit doesn't help considering how much more relaxed it is compared to her Sinnoh outfit. Turns out she just wanted to battle the fellow dragon trainer and was too nervous to ask, but still...
Alain from the Mega Evolution specials had no real motive to enter the Kalos League and was not collecting badges until he met Ash and his particularly special Greninja. Come 2 episodes before the big event, and Alain has alreadycollected enough badges to enter the league. His motive to do so? Just to fight Ash. Weirder still is how Alain has the special benefit of just walking to a trainer and ask for a battle, but he makes the occasion very important just for Ash. The fact that he even comments that he never felt this strange feeling until fighting Ash, and he was seen smiling from this. Mind you, he has been scowling ever since Act 4, and it was fighting Ash that brought him smile.
Clemont has been thoroughly inspired by Ash, always looking up to him. Ash meanwhile is ever impressed by Clemont, and is even fascinated by his inventions. Ash never showed negativity towards his leanings on science (something even Bonnie showed frustration). And there's that angst he had, thinking he "couldn't satisfy" Ash in battle which leads to him leaving the gang for a while. The gym battle itself is Clemont dedicating himself towards Ash. And then there's the insert song "Kira Kira", which is referred to as Clemont's character song, a song about him being inspired by Ash and saying how much Ash means to him.
Sawyer adores Ash and sees him as a role model, but the defining moment was definitely him repeating Serena's words of "Welcome back, the one I admire" during their final battle, when he realizes that Ash no longer is down after loss to Wulfric. Considering that context of the situation is the same as Serena's and Serena's status as Love Interest means that he definitely saw Ash as more than friends or rivals.
Professor Sycamore manages to sniff out Meyer's secret identity as Blaziken Mask by... inhaling the scent of a dirty oil-stained rag (and commenting on 'the fragrant flavor of oil' in the process) that Meyer had asked for, and later identifying the same scent on the Keystone Blaziken Mask lends him. When Sycamore next approaches him, he does so while commenting on how he never gets sick of the smell in a very sing-song, flirtatious voice, leaning into his personal space, and saying he wants something else from Meyer than just repairs.
During a festival in Sinnoh, Brock gets a lovey dovey over what appears to be a shady male guy and flirts with that guy. However, this shady guy actually turns out to be Officer Jenny in disguise, meaning that Brock saw through her cover.
The introduction of gender differences in some Pokemon into the anime's canon has actually unintentionally retconned Ash's Butterfree into possibly being homosexual in the episode "Bye Bye Butterfree". Ash's Butterfree ends up finding another Butterfree as a mate, and neither of them have the characteristic spots on the lower parts of their wings◊ that female Butterfree have. Making the other Butterfree pink was likely meant to imply its gender, but the existence of Pokemon with exotic colors in the anime (including Butterfree itself), coupled with the established idea that people have assumed a Pokemon's sex before only to be wrong, means that the possibility of Ash's Butterfree mating with another male is still there. This was most likely due to the fact that this episode was written before the mechanics of Pokémon gender differences and shiny Pokémon were even thought of and introduced. Pokémon: I Choose You! recreates the events of this episode and properly depicts the pink Butterfree with wing spots.
Ash and Cilan get this with Cilan's very campy nature and Hero Worship of Ash, which often comes off as obsessive or romantic.
Mallow is very protective of Lillie in the anime, always encouraging her to get over her fear of Pokemon and even dragging Ash into spying on her at one point. A promotional image for a plot involving the Ultra Beasts even has them holding hands while surrounded by Xurkitree and Blacephalon.
In Pokémon SM058, an alternate color Toxapex (colored to resemble James when poisoned by his Mareanie) tried to give James a Corsola Horn. Which is popular among female Mareanie (and presumably among female Toxapex as well). After both fought over James'sfemaleMareanie and James saved both the alternate color Toxapex and Mareanie from a Tentacruel who lunged at them. The alternate color Toxapex is male. James is male. James's Mareaniewho is also smitten with Jamescaught on, chasing after the alternate color Toxapex as he was chasing after James with him smiling and blushing all the way. Instead of trying to help her teammate, Jessie watched as both Pokémon hobbled after James and called him a stud. A stud among Mareanie and Toxapex, female and male.
It isn't just Lillie that Mallow seems to be shipped with, as she's also shipped with Lana, as episode 59 revealed that they've been Childhood Friends, even holding hands a few times as small kids! Also, during Kukui's wedding, they were seen celebrating pretty close together, and there's even subtext between the both of them in the manga version as well.
How I Became a Pokémon Card features one chapter with two boys who have a very close friendship and constantly blush around each other; it doesn't help that one of them is a trans boy, and his friend didn't believe him in all his years he knew him.
Pokémon Adventures has its fair share of Ho Yay moments. In the FRLG arc, fans have taken to pointing out that Green is Red's coathanger. Gold and Silver had some rich Foe Yay vibes in the GSC arc when they first met, and by the end of the arc has Silver tearing up a little when he thought that Gold was lost in the timestream. It culminates to the point that Gold blushes when Silver reveals that he was conscious when Gold called him his friend in the Emerald arc. Dia and Pearl need no explanation, and their brief falling out in the middle of the arc can almost be taken to be a breakup.
Satoshi and Shigeru in Pokémon Zensho have the same Foe Yay as Red and Blue in the games. To top it off, at the end they have a sincere moment and end up becoming friends again.
Video Games (general)
You can literally invoke this to most of your Genderless Pokemon! If you bring one (like a Metang) to a Daycare Center together with a Ditto (another genderless Pokemon), you will eventually receive an egg containing a non-Ditto baby (for this case, Beldum).
You can also invoke this in Pokemon-amie with the corresponding gender.
Red and Blue. Blue's description of having been your friend gone rival makes him sound Tsundere toward Red, you have Foe Yay for most of the original games, and once you go back to being friends he seems to think about him a lot.
In the original Red/Green/Blue/Yellow versions, the Lass trainers comments to the player also are either flirting with you or accusing you of being creepy towards her. In FireRed/LeafGreen these are unchanged if you play as Leaf.
The original Gold, Silver, and Crystal contain a strange glitch-induced example. Kurt could make you several unique Poke Balls with unusual effects if you gave him Apricorns, but many of these balls were glitched to have effects different from those intended. One of these balls, the Love Ball, was a Situational Sword intended to give a catch bonus if the targeted Pokemon was the same species and opposite gender of the player's (presumably to show off the then-new breeding mechanic)... but the bug caused it to get the bonus on Pokemon of the same gender instead. Buggy Ho Yay ensues!
The Ferris Wheel Date Moments are full of Does This Remind You of Anything? in the Japanese version. Two of the characters you can date are of the same gender as the protagonist - Waitress Aurora for the female protagonist and Hiker Andy for the male. Andy comes off as a Hard Gay who constantly talks about the heat and asks you if you've ever had a lover (in context it sounds like he's seducing you). Aurora sounds like she's coming onto you, though the Japanese version has her talking about a boy. In the English version the Les Yay was upped due to lack of reference to the boy and in the French they made the boy into a Pokemon of hers.
Not to mention everyone taking N and Hilbert's ferris wheel scene as Ho Yay as well.
Expected, since N has a lot of romantic subtext with the protagonist regardless of gender, it only gets more overt in the sequel, with N saying lines like "There is also a Trainer I want to tell how I feel..." obviously referring to the protagonist of Black and White.
The female protagonist in Black 2 and White 2 can get a ferris wheel date with a rocker girl, who would sing a surprisingly romantic song to her while on the ride. She'll also say that she can only show her true image around you, and will sing more for you next time she meets you.
Hiker Andy returns as a Ferris Wheel encounter for the female playable in Black 2 and White 2... but all he wants to talk about is his great romance from two years prior (the previous games).
One of the male backers in the Small Stadium will claim that he "wishes that the athletes would fight over him the way they fight over the ball". This is the case even when the athletes in question are the male Hoopsters instead of the female Smashers.
In Black 2 and White 2, when they visit Join Avenue, Elesa keeps up the trend of looking for stores run by dazzling cute girls while Marlon asks for stores run by very energetic men.
Speaking of Elesa, there's her rather popular shipping with fellow gym leader Skyla. They are canonically close friends...
X and Y
If you play as Serena instead of Calem, Shauna's very visible attraction to the player character remains. This can get delightfully yuri-ish during such wonderful moments like the emotionally-charged fireworks cutscene at the palace.
Also, after the butler watches you and Shauna, he gives you TM17, Protect. Even the butler can sense it.
There is a Brains-and-Brawns Double Battle formation with a male Martial Artist and a male Psychic trainer (Trainer names Frank and Sly). When you win, the Martial Artist will cry and the Psychic will try to comfort him in a surprisingly tender fashion.
Lumiose City's (female) hairdresser will get rather... distracted... by the cute looks of your female player character once you raise your hidden Style rating enough and become a 'regular' customer. She'll also start making more small talk with you while asking you how you want your hair done, and one of things she can do is compliment you on your choice of fashion.
If the player goes to the Transportation Services building in Lumiose City, they can go to the second floor and talk to the NPCs who work there. One of them, a blond man, will be startled and proclaim that you shouldn't sneak up on him like that and that his heart is beating so fast because of you. If you talk to him again he'll claim he's not in love with you. He'll say this to the male player character as well as the female one.
Professor Sycamore is so enamored by Lysandre's "passion" when he angrily explains to the player how unjust the world is, the idea Lysandre alludes that genocide was a viable option to deal with it seemed to fly straight over Sycamore's head. The fact they're said to have had a friendly past together does not help quell the shipping that ensued.
Sycamore: What a passionate person. He's just like a blazing flame.
Gen III and ORAS
Sr. and Jr. Anna & Meg. If they call you in Emerald, you'll speak to Anna, who says that both Meg and Pokémon are "so cute!". The two will then have an argument during the call, where Meg complains about being Anna's slave, and then Anna gives you this lovely quote:
Anna: "I wouldn't treat you like a slave, Meg! You're too special to me!"
The same couple in Omega Ruby/Alpha Sapphire (now called Teammates) have much more romantically suggestive dialogue about one another when you first encounter them.
A pair of NPCs appearing to be of the same Trainer Class shows up on Sea Mauville in the remakes inside a room that requires a key to enter. When talked to, the senior demands to know how the player character got in, as she was certain she locked the door, while the junior just blushes.
Lisia can definitely come off like this when the character is female; constantly spurning Chaz's advances, blushing around the player character, and seeming to very interested in their Coordinator career. Not only that, when the player first beats the Hyper Rank contest, she nervously suggests the player and she do 'something' that she can't elaborate on due to Chaz being a Moment Killer.
Wally is this in spades in the remakes, if you play as Brendan. Gaining an actual personality from the remakes may have helped, but the fact that Wally is super moe, constantly blushes and around you and is more nervous than Hinata confronted with Naruto gives off strong waves of a crush. It doesn't help much that his proposition to be your rival sounds a lot like a love confession.
This, and his strong relationship with his first Pokémon and team ace (A male Gardevoir in R/S/E, a Gallade in the remakes), both Pokémon renowned for the bond with their Trainer.
This conversation between an Ace Trainer and a Delinquent you find in Mauville City, both female. If nothing else, it sounds like a breakup:
AT: "Eh? Seriously, ma'am? Ya gonna treat me to dinner?"
D: I told youse I would, eh? Ya managed to become an Ace Trainer, doll. We gotta celebrate somethin' like dat. Pile up as many o' dem Village Sub Combos or Magnemite Croquettes as ya want.
AT: Thank's ma'am! I'mma take you up on that!
D: Yeah, kid. You do dat. But dis'll be our farewell meal, y'unnerstand? Youse can't keep hangin' out wit' a hood like me- not even one with a fab do like mine. Not wit you bein' an Ace Trainer an' all.
Like noted above, the characters are given a little bit more personality and hints of their relations with others in the remakes. Some of it stays All There in the Manual or is integrated into the dialogue in reasonable ways, such as Flannery saying she heard about something from Winona. Then Brawly shoehorns Granite Cave into his after-battle conversation seemingly so he can point out how "my friend Steven" rushed there after being told about it. (The German version somehow adds to this despite translating the above quote as "meinem Bekannten Troy" - unlike "Freund", Bekannten could mean boyfriend regardless of grammar issues.note "Ein Freund" is always accepted as strictly platonic. "Mein Freund," though literally the possessive form "my friend"... People learning the language are typically recommended to use "mein Freund" and its feminine form "meine Freundin" sparingly (if at all!) to avoid accidentally calling people their girl/boyfriends left and right, despite the term technically being ambiguous.)
It's hinted at that Steven and Wallace are closer than first thought. At the end of the Delta Episode, one of the many cutscenes show Wallace talking to Steven at the Pokemon League. Steven says he needs to learn more about the world, and asks Wallace if he will be by his side when he does decide to pursue his dreams. Wallace says he will be there when the time comes.
The official Japanese Pokemon Twitter account has posted "this", regarding Archie and Maxie's relationship. A rough translation of the last sentence: "Somehow, their relationship seems pretty good!"
Pokemon Sun and Moon
One of the trailers for the game showed an older Red and Blue hanging out together by Alola's new Pokemon League. Fans immediately decided they had come to Alola for their honeymoon. It doesn't hurt that they have dialogue reminiscent of Like an Old Married Couple...by which we mean Red says "..." and Blue says "As silent as ever, eh?"
If you choose to play as a female protagonist, many of Lillie's interactions with the player character can come across as this. The most blatant case is during the credits sequence, where she appears to be about to give a Love Confession before being interrupted by fireworks.
There's also an earlier scene on Exeggutor Island where the two of you end up in a cave together seeking shelter from the rain, where Lillie is also about to say something very very personal to you when the rain stops. Then, big giant rainbow.
For most of the game, Gladion treats Hau as a carefree idiotic boy who can't take things seriously....only to reveal to the player at the port that he considers Hau an interesting kid and that its admiring how he doesnt feel overshadowed about being Halas grandson.
Also, regarding Gladion. For some reason he's perfectly fine with Lillie and the protagonist's constant Ship Tease but gets angry after Hau praises Lillie's new outfit.
At the Poni Plains there is a Male Ace Trainer (named Cole) who gives out the TM for Quash and after defeating him he will refer to the player as "babe" and "baby" regardless of their gender.
There's this line Gladion says to the player (regardless you play as a male or a female) during the Champion Challenges.
"What does a Pokemon Trainer really need to be succesful? I guess everyone might have their own answer. But for me....I want the strongest rival for myself."
When the player reaches Po Town, they can find two Team Skull Grunts waving at each other from opposite sides of a hedge. The first one waving will say "What's wrong with that guy!? Doesn't he realize we're being invaded!?" The Grunt from the other side? "What is wrong with him?! Why does he keep on staring at me? Does he see how hot I am or something?!"
Also in Po Town, if your character is a girl you get a female Skull member calling you cute and another one asking if you're "looking for a battle in a romantic spot".
Hapu outright forgets to give the player a ride Pokémon earlier in the game due to being "taken aback by Lillie and how lovely she was."
Pokemon Mystery Dungeon Explorers
The relationship between Guildmaster Wigglytuff and Chatot is far more than platonic. At first it seems Chatot's apparent crush (from travelling with him for so long and respecting him) on the Guildmaster is one sided as Wigglytuff seems apathetic to the idea of spending time with Chatot on the expedition. However, when Chatot risks his life to save Wigglytuff, Wigglytuff is in tears and tries desperately to help him. It happens again when the player and partner get attacked by Kabutops. Wigglytuff is just barely holding it together and calls Chatot his invaluable partner, to which Chatot is delighted to hear it. It's implied Wigglytuff nursed Chatot back to health after the heroes leave for the Hidden Land.
Speaking of the player and the partner, depending on their gender, the game plays out like a love story/triangle between them and Grovyle too, who seems to trust each other more than anyone else. Grovyle even says "Parting hurts" which could be taken as the loss of their significant other. The player/partner relationship is played out like a couple in that everyone seems to call them the greatest of combinations, the Partner cries a river when the player Disappears into Light, the Partner constantly tells the player how much he/she gave him/her strength and can barely keep it together when the player supposedly disappears forever. They even play mommy and daddy to the baby Manaphy and are very concerned when the player seemingly gets trapped in a nightmare made by Darkrai.