In the world of soccer
In Sayonara Zetsubou Sensei, the professor is trying to explain that if certain people were to lie, even as a joke, those surrounding them wouldn't get it. To make his point, he's showing people saying things they wouldn't usually say. Among them, there's an Hyuga Kojiro, the ace striker of the Captain Tsubasa manga, saying that he wanted to be a goal keeper...!
In Mr Fullswing, the main protagonist Amakuni Saruno is talking about the scenario he had planned for himself, most of his ideas are coming from other mangas, and one of them is that he was supposed to be friends with the ball, a direct reference to one of the principle of Captain Tsubasa.
In Yu Yu Hakusho, the main character Urameshi Yusuke is sacrificing himself to save the life of a young boy who was going to get hit by a car. The boy was also playing with a ball, and we know at the very beggining of Captain Tsubasa that Tsubasa was hit by a car as he was playing with a ball. Still not convinced? We'll learn later that Yusuke sacrificed himself for nothing, because the boy was going to get hit but would have been saved miraculously by his ball anyway. It's hard not to see Tsubasa's story here.
Sometimes manga artists like to draw illustrations with famous, present or past famous mangas characters. The illustrator of Eyeshield 21, Yusuke Murata made such a color art, and of course, Captain Tsubasa is represented by his main character, Tsubasa, when he was younger, with the Nankatsu jersey.
In Tough, a fighting manga, Kiichi Miyazawa, a.k.a. Kibô, the main character, is trying to hit an opponent, but doesn't get a clean hit. His comment afterwards is a clear enough reference as it is.
In Kakukaku Shikajika, an autobiographical manga by Akiko Higashimura the author and thus main character is also making a clear enough reference.
In B Gata H Kei, a comedy 4 coma manga, the main character is a female pervert trying to have sex with a guy, but that guy is a blockhead, and she's actually awful at trying to get what she wants. Going with him to a park (the kind where people make out and more), she's passive at first but then her inner "erotic spirit" gets fired up and tells her that before she was much more assertive, and now she's a tiger without fangs. And if you think that reference isn't clear enough, the panel displayed here should completely erase any doubts.
In Watashi ga Motete Dousunda, the main character, Serinuma Kae, an otaku girl (you could even call her a fujoshi) is asked to help the girls soccer club. She accepts, even though she never played soccer in her entire life, and is asking for the help of Nanashima Nozomu to get better, giving him arguments like she's "friend with the ball", and obvious reference to Captain Tsubasa (even though one sign is censored).
In Himouto! Umaru-chan, the situation is a bit similar, except it's side-character Sylphinford Tachibana who's asking otaku main character Umaru Doma to help her train. The reference is the same since Umaru is teaching her to be friends with the ball (and they're taking photos of them with the ball), but she's taking it to the next level, teaching her that the ball is their boyfriend as well, as we see them running on the beach at sunset with the ball, a cliche you'd usually see with a couple involved in a romantic relationship. In the next chapter, you can even see Sylphin skating on two soccer balls: was she inspired by Michael who's doing the same with one?
Probably one of the first reference ever made, as Cat's Eyes was published around the same time as Captain Tsubasa. When Hitomi Kisugi is challenging a man to a game of golf, she does the same reference as most of the mangas shown in this section. Not just a coincidence since Hitomi is clearly saying that it was already said before!
This one is probably one of the first reference as well, in 3-nen Kimengumi, the main character Ichido Rei manages to win a pool race against all odds by distorting the water, and thus, reducing the distance he has to swim. How the hell did he mange to do that? Well, the author Motoei Shinzawa simply explains that to do that, you need to be friends with the water, and Rei talked to the water to do his bidding. That explanation is causing readers to throw objects at the author, who promise he'll never use that again. Obviously, because that was already used before, and is a poor excuse to explain someone's abilities!
In Jitsu wa watashiwa, the main character Kuromine Asahi is hearing his friend Okada Kanade about his confession to Akemi Mikan, because of various reasons (love triangle and things like that), the latter is angry at him because of it and thus keeps on kicking him to the head... Leading to an obvious joke and reference related to Captain Tsubasa from the main character.
In Seshiji o pin! To ~ Shikakou Kyougi Dance Bu e Youkoso ~, during a flashback of the character Yamaki Sho, one of the senpai of the main characters, we learn that he tried many sports before competitive dance, one of them being football. A representative of each club is trying to get him back, and the soccer player is asking him to revive the golden combi they were forming since elementary school. Not only that, Yamaki answers that he'll think about it, if he can be Tsubasa. The soccer player is confused though, and Yamaki eventually rejects him under the pretense that he can't be together with a guy who doesn't know about Captain Tsubasa. You can't be more obvious than this!
The manga Haikyu, by Haruichi Furudate, is about volleyball. The main characters and their teams play against many opponents, and one of these opponent's team is featuring twins, the Miya twins, and they referenced the Captain Tsubasa's own famous twins. After performing a good combination play in which they reverse their roles, the spiker becoming the setter and the setter becoming the spiker, they feel like they could also be able to pull off one of the Tachibanas twins' trademark move: the Skylab hurricane! Only to quarrel about who'd be "bottom" if they did.
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