In Rosario + Vampire, at the beginning of the 5th episode, the hero Tsukune has a "fantasy" going about football, the references couldn't be clearer: uniforms similar to those of Nankatsu and Toho, a Drive Shoot, many players are clones, we can find Sawada Takeshi in Toho, Ishizaki, Manabu and Kisugi on Nankatsu's side...

In the first episode of Eyeshield 21, Mamori tells Sena that he should join a club, and when he's thinking about the clubs he could join, he's starting to imagine a situation if he was in the football club: he's facing a keper named "Wakashimada", very close to Wakashimazu don't you think? If you don't think it's a reference, then there's still the Drive Shoot (Tsubasa's shoot) that he's failing miserably...

The One Piece movie entitled Chinjuuto no Chopper okokule (Chopper's kingdom on the strange animals island) has a featurette on soccer. Luffy and his special shot, the Gomu Gomun no Shoot could already be considered a reference to Captain Tsubasa's special shots, just like the balls going through the net, but if you're not convinced, you just have to hear Usopp shouting Drive Shoot when shooting with all of his strength a ball that will just slowly roll towards the goal and eventually get in.

The 106th episode of Gintama is dedicated to football, Gintoki Sakata is assembling a team with the characters of the anime to replace a football team that Kagura has poisoned by accident. Katsura and his giant white chick pet Elizabeth are wearing in the locker room uniforms of Nankatsu and Toho with Elizabeth going as far as having the same hair and skin color as Hyuga, then at half-time, they'll respectively dress as Misugi and his girlfriend Yoshiko... Otae and Isao will also perform a Skylab Hurricane in the second half's loss time. We can also see a special type of combination close to what Aoi did to one of his partner...

In the 7th episode of Dororon Enma-kun Meeramera, a reboot of the Dororon Enma-kun TV anime series, there's a demon causing everyone to slip. When the newscaster is showing everyone slipping, there is a picture of a football game, and while everyone is upside-down, their uniform are clearly Toho's and Nankatsu's, skin tone and numbers would imply that they are indeed Tsubasa, Misaki and Hyuga, even the keeper has a uniform and hat similar to Wakabayashi.

In Gintama again (1st episode of Porori-hen) Kagura has a boyfriend, her father Umibozu and Gintoki the main character, eventually decide to accept it and act like "grown ups", but they're taking it too literally and just end up with huge bodies, referencing the huge bodies Captain Tsubasa characters have with Takahashi's peculiar drawing style, which is also a popular meme on internet.

In the 40th episode of Digimon Adventure the protagonists are playing soccer with their digimons, and the latters are finding it quite difficult to understand, but Agumon will eventually shout the famous leitmotiv of Captain Tsubasa, in other words: that the ball is a friend.