It helps there is only one Official Couple, and it has two different out comes.
The scene between Someoka and Fubuki in the second season episode pictured on the right is the more glaring example.
That's just the start. If one notices closer, they stand beside each other on nearly every single time they are shown on screen. And then there's their interactions. And there was that Dark Emperor Match, where it sounds like they are dealing with a bad break up.
Let's not miss the movie: The Strongest Army, Ogre! where Fubuki who came from the future ends up wearing Someoka's uniform.
Endou and Domon gets a moment as well, when they were talking about stars and planets and where Aliea Academy came from, cue both of them running together smiling at each other across space towards the Earth.
The seiyuu seem pretty keen on it too!
Kaji thinks of Kidou, Sakuma, and Fudou's relationship like a love triangle, with Sakuma being "the jealous girl".
He also comments in an interview alongside Konno (in an article based on their characters) that "if Ichinose and Domon were a boy and girl, they'd make a good husband and wife".
Hiroto and Midorikawa. Saginuma sometimes is depicted in a love triangle with these two. Also, Burn and Gazelle.
Hiroto/Midorikawa is fueled even further when Midorikawa appears in GO as Hiroto's personal secretary.
Tsunami and Tachimukai manage to appear in almost all of the official art together, normally hugging or touching; and in the anime they have plenty of ho yay inducing moments, mostly due to Tsunami acting as Tachimukai's Big Brother Mentor.
Endou and Kazemaru are stated to be childhood friends. They also sit and stand together very often compared to other characters.
In the show's second season Endou was very affected by Kazemaru leaving the team.
If you think about it, the only difference about the consequences of the first fight with Genesis in both anime and game was that in the game, iKazemaru had to leave the team due to receiving a beat down while in the anime, he had a heroic BSOD and left on his own. Endou only had the Heroic BSOD in the anime. This implies that the only reason Endou was too depressed to even touch a soccer ball was because Kazemaru left the team on his own free will.
Then there's also Kazemaru's constant sacrificial play for Endou.
"I have to do something, before Endou...!"
Then there's that whole episode on the Dark Emperors...
In the show's third season, after they won against Little Gigant Kazemaru was shown hugging Endou around the waist as the team yell in celebration.
What? Nobody mentioned Dark Emperors!Max and Dark Emperors!Handa yet? Did you guys even see Revolution V? This tropette nicknames it "Gay Tornado".
Everything Gouenji and Endou do in the same frame together is shipping fuel. Literally everything.
Taken Up to Eleven in GO when every time they're shown it seems like they're dealing with a bad breakup.
Fudou and Kidou enter this realm shortly after Fudou's Heel-Face Turn. Especially after Kageyama's death when — in the videogames — Kidou gets a Cry Cute moment and Fudou seems to be comforting him.
Then there is the moment when Killer Fields was created.
A mild one, but Aphrodi seems very interested in Fubuki when he joins the team. So much, that he plays an important role in motivating Fubuki to get out of his Heroic BSOD. Aphrodi gets injured during Raimon's match against Chaos, but Fubuki visits him in the hospital and thanks him for his help.
Inazuma Eleven GO
There is Tsurugi's "interest" in Tenma which starts out as Foe Yayuntil he makes a Heel-Face Turn. After which Tsurugi can almost always be seen next to and of near Tenma and he generally cares about him to the point where he helps Tenma release his keshin and is very satisfied with the results. Tsurugi also chose Tenma as his partner in the Fire Tornado Double Drive hissatsu, as he believed Tenma was the one to change him.
Not to mention Tenma loves glomping Tsurugi.
Since Tenma and Tsurugi are the Expy of Endou and Gouenji, everything that they do altogether in the same frame altogether is also a shipping fuel.
Also there is Taiyou and Tenma which doubles as Foe Yay only without the animosity. Taiyou had been interested in Tenma ever since he first saw Raimon's match on TV. It was implied he and Tenma were similar to each other in their love for soccer. Tenma had a Heroic BSOD after he realized Taiyou was risking his own life to play against Raimon. After the match against Arakumo, Tenma and Taiyou hold hands, promising to each other that they'll play together again someday.
In the game, there was a scene where Tenma saves Taiyou, who collapsed and fainted on the sidewalk and later at the hospital, Taiyou gives encouraging words to Tenma.
KMC (one of the singers for the opening themes of the series) has even written a song dedicated to their relationship titled "Me and You and the Wind and the Sun".
Shindou and Kirino, they are almost always together and Kirino is always concerned about Shindou's well being especially after Shindou is hospitalized.
Nearly everything Kirino says in the game is related to Shindou in some way. This is not an exaggeration.
Kirino and Kariya, after they get over the Foe Yay. They seem to cooperate quite nicely.
In Chrono StoneKariya easily reads Kirino's mind on how he's jealous of Shindou's strength. He later gives up his seat for France to Kirino (when Daisuke wouldn't normally change his mind) by claiming he had a stomachache.
Hayami and Hamano, who hang out often and also balance each other out in personality. The one running shop even found it odd when one afternoon she saw Hayami fishing but not with Hamano.
The word-for-word intent of Mahoro when he avoided Amagi all those years ago: he wanted to protect the smile of his first friend.
When Amagi was troubled about not knowing anything, Kageyama Hikaru comes up to support him and continues to be concerned about his senpai during the Genei match.
Hikaru continues to comfort him in the rain when he is surprised to see that Mahoro is the captain of Gen'ei and completely different then the childhood friend he remembers and holds an umbrella over him and helps him find a way to excert his pent up stress (AKA screaming) and it was adorable.
Tenma and Shinsuke became best friends so quickly you'd think they've known each other their whole lives.
Yukimura's reaction when he thought Fubuki betrayed him makes it look like he has a crush on his coach.