Pokémon/Ho Yay

Anime

 * Dawn and Zoey's relationship in Pokémon 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.
 * Also, regarding the ambiguity of Ash's Pikachu's gender, the argument for "it's male" is rather long, while the argument for "it's female" mainly consists of the fact that it does not return the feelings of Dawn's Buneary, who has a crush on it and has been confirmed as female (the existence of said crush in the first place is part of the argument for male), and that Ash's Bayleef, who has a crush on Ash and has also been confirmed as female, sees Pikachu as a rival for Ash's attention. You see where this is going, right? (Bulbapedia even treats its status as "confirmed male in dub only", which reaffirms this position.)
 * To further compound this, a recent episode had a female Togepi's Attract working on Pikachu, meaning it's male, if Attract works the same way in the anime as it does in the games.
 * 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 * Morty spends nearly all of For Ho-Oh the Bells Toll withdrawn and sullen.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 appearence 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*
 * Is this troper the only one who sees Some thing between Ash's Pikachu and Dawn's Piplup? (Granted that ending includes the other Pokémon too but still). If not, they're at least Heterosexual Life Partners or Those Two Guys.
 * This scene, where Seymour hugs Ash for saving him.

Manga

 * Pokémon manga are not exempt from this trope. 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 biologically a girl, and his friend didn't believe him in all his years he knew him. Pokémon Golden Boys has Gold and the Ambiguously Gay Bugsy.
 * Pokémon Special 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.
 * Magical Pokémon Journey does have Squirtle who has a crush on Almond. Charmander is quite obsessive about Eevee and is implied to have a crush on him.
 * 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

 * 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.
 * The ferris wheel dates in Pokémon Black and White are full of Does This Remind You of Anything in the Japanese version. Two of the characters you can date are the opposite 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 boy 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.