In the anime, Zangief from Street Fighter appears among the crowd of people trying to be Genkai's successor (His chest hair is replaced with Sagat's scar). Other Street Fighters cameos include Dhalsim, E. Honda, and characters that resemble Ryu, Ken, Chun Li, and T. Hawk. In the Korean manga translation, Kaito tells his girlfriend to stop spamming Shoryukens.
Yusuke briefly makes a Virtua Fighter winpose in the Makai Tournament. His appearance becomes blocky like the game's characters as well.
The three demons that try to attack Keiko when Yusuke is unconscious are based on characters from the Journey to the West, as there is a kappa, a monkey demon, and a pig demon.
Team Uraotogi's members (with the exception of Suzuki), are homages to Japanese folk tales and legends. Though coincidentally his dub name is the same as Suzuka Gogen.
The Four Saint Beasts are based on the Guardians of the Four Directions in Asian mythology.
Kuwabara's favorite band Megallica is a portmanteau of Megadeth and Metallica.
Kazemaru sings Highway Star by Deep Purple (poorly...), in the Viz translation.
When Juri recovers from the Idunn Box's effects her transformation sequence is based on that of Sailor Moon. Also, in the Viz translation, Kurama once says "Just call me Tuxedo Mask..." while throwing a rose. Koenma's disguise in the Makai Tournament closely resembles Tuxedo Mask as well.
In the last episode, there is a truck with the world Narlboro, written on it, as a reference to Marlboro
In the Viz translation, Carl Lewis is mentioned by Byakko, as he mockingly tells Kuwabara to jump farther than him.
Karasu's hair, when powering up, turns blonde in a manner similar to a Saiyan from Dragon Ball Z. In the English dub, Koto makes a shout out to Dragon Ball Z in response to seeing this form.
In Episode 77, Koenma rides a small cloud similar to Dragon Ball's Nimbus Cloud as he's about to leave the Spirit Realm.
In the English dub of Crayon Shin-Chan, Hiro (who is also voiced by Chuck Huber), yells Sword of the Darkness Flame! while carrying a normal bamboo sword.
Hiei, Kurama, and Yusuke appear as figures in Hunter x Hunter
Pu also makes an appearance in the Hunter x Hunter 2011 remake in episode 41, where he is shown as keychain figure attached to Neon's phone.
In Bobobo-bo Bobo-bo, Don Patch uses the Spirit Gun to defeat Master JOY.
In the pilot of Sket Dance, Switch invented an eavesdropping device called Tobikage that resembles a Draco, or a flying lizard. The kanji used for Tobikage is the same as Hiei's name.
For a short time, the unnamed blast technique that Chad uses in Bleach was nicknamed the "Reigan" by fans.
In the first Naruto movie, Dotō Kazahana, the main villain uses a technique that is extremely similar in name and appearance to the Dragon of the Darkness Flame, with the main difference being that his dragons were composed of ice.
Though it may be coincidence, Deveganizing Ray in Scott Pilgrim vs. The World resembles Yusuke's Spirit Gun (moreso in the movie).
The Nine Tail Fox from Naruto was later given the official name of Kurama, which was intended as a tribute to Yu Yu Hakusho's Kurama.
In Clannad, many female characters resemble Keiko. There is mention of a character named Yusuke and a baby boar named Botan.