These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Teshima and Aoyagi are popular with how high their positions are in the poll.
The whole Hakone team, but especially Toudou, Arakita, Shinkai and Manami.
Even the Guys Want Him: Imaizumi loves mentioning that Naruko's fans are mainly guys, and as shown in the third day of Interhigh, while catching Sohoku up to Hakogaku, both the girls and the guys were watching him in awe, almost as if they had fallen for him.
Foe Yay: The most popular ones are Makishima/Toudou, Imaizumi/Naruko and Kinjou/Fukutomi.
Machimiya/Arakita also counts.
When Toudou and Onoda first meet, Toudou tells him he considers him "a 3, visually speaking". After the race, Toudou takes it back and says Onoda has nice eyes, which makes Onoda blush.
Very much so between Onoda and Manami. In a conversation with Toudou, Manami calls Onoda's smile "beautiful" and comments that his glasses suit him. Onoda is also rather mesmerized by him, and at times seems distressed by the thought of not going to Interhigh because he wouldn't be able to fulfill his promise with Manami. The vibes go over the roof when Manami pulls Onoda close during the race and asks if he "can feel it too". Arakita even shouts to Manami to stop "whispering with the enemy". These two are not playfully compared to Shinji/Kaworu without reason.
Hell Is That Noise: Midousuji makes the absolute worst noises, especially when contorting his body. He would fit in a horror anime much more than in a sports series.
Aoyagi and Teshima have an almost psychic connection and spend all of their time together.
Makishima and Toudou have each other's phone numbers and talk all the time. When a teammate overhears Toudou talking on the phone with him, he asks who "Maki-chan" is and if it's one of his fangirls. He replies with "Something like that".
Naruko and Imaizumi's relationship as rivals and friends has some of their situations make a certain kind of fan happy. It's taken up further when on the third day of Interhigh, Naruko collapses after catching Makishima, Onoda and Imaizumi up to Hakone, Imaizumi is so touched by the effort that he swears he'll win the race. But not for himself, or the team, but for Naruko.
Socially awkward Makishima is more comfortable around Tadokoro than pretty much anyone else, and they have an easy relationship; if you see one outside of club activities you probably see the other as well. "Tadokorocchi" is also the only person Makishima's nicknamed, and based on his internal thoughts in one omake he finds Tadokoro's "bear" qualities cute.
Izumida's behavior towards Shinkai makes it look like he has a crush on him. He admires Shinkai deeply and sees him as a role model, looks very disturbed once Shinkai gets disheartened over his loss to Midousuji, and even describes Shinkai as "beautiful" and "strong".
The anime omakes also take Ibitani's admiration of Machimiya Up to Eleven, to the point of having him gushing"Miyaaaaaa!" over everything Machimiya does and even peeking and crying when Machimiya breaks up with his girlfriend.
For Makishima as well. When Tadokoro gets left behind on the second day of the inter-high, Makishima makes the decision to go on without him. Onoda asks Makishima to let him stay behind and help Tadokoro catch up, which he releuctantly agrees to once he sees Onoda's Puppy-Dog Eyes.
THE PACK: the mass of cyclists who failed to get high rankings places on day 2 of the Interhigh and so are now riding as a huge group to ride at a high consistent speed to catch up to the other cyclists... that is played more or less as an unstoppable eldritch horror in the anime.
Arakita's withdrawn from the team in the third day of Interhigh can have this kind of effect for some, mostly because his teammates act like he died or something (Manami is especially guilty of this, going to the point of saying Arakita was a great person. In the past tense). But for the majority, it's still a very convincing Tear Jerker moment that crowns his Character Development, so there is a bit of Narm Charm element there.