Many fans say the first stage has some similarities to Gunbuster and DieBuster, as the gohma carriers and gohma lashers look like the Space Monsters from that series.
The way Gohma Vlitra first appears by popping out of the planet earth similar to how one of the space monsters from Diebuster episode 4 emerges out of Jupiter. Gohma Vlitra itself has been noted as looking similar to Sin and Lavos.
One of Asura's later forms where he glows completely red and his four extra arms become gigantic limbs is possibly one of these to V2 Jinchuriki forms from Naruto. It helps that CyberConnect2 makes the Naruto Ultimate Ninja Series.
Not to mention that the cause of this form is the death of a girl before his eyes. After the village was reduced to a crater by a massive Death from Above attack. Add to that the reddish black energy colon and a beam not unlike the Bijū Dama, and the entire scene is remeniscent of Konoha's destruction by Pain followed by Naruto's transformation.
Likewise, the clash between Wrath Asura and Yasha in chapter 15 is a reference to Naruto and Sasuke's clash at the valley of the end.
Wrath Asura feels like Guts possessed by the Black Beast in his Berserker Armor.
The mindlessness of the form as well as well as not really being all that effective against the main rival might bring to mind of Haseo's B-ST form from the .hack//G.U. Games movie. His one Jump attack he does is similar to B-ST Haseo's opening attack on Ovan.
The end of the first set of episodes is a scene where Asura is falling down in darkness as blue lights fly upwards. This is a scene very similar to the Game Over screen of Silent Bomber, the second CyberConnect2 video game.
Amaterasu from Ōkami makes a cameo in two of the illustrated interludes between Episodes.
Sagat and a cat from Monster Hunter appear in the same interlude Ammy is shown the most notably in, Episode 10's interlude.
The PAX mecha from the first Lost Planet can be found in the interlude for episode 1.
Yasha's fighting style —quick, acrobatic, slashes dudes apart with his hands and feet— is very much like Rei's Nanto Suichōken from Fist of the North Star.
The Kagebosh mooks have a move where they stretch their arms similar to Dhalsim
One person noticed that Durga looks a lot like Mind Controlled Chun-li when she has her hair down from the Street Fighter II Anime.
In episode 15, along with the clash, the soundtrack used in the first part of the battle between Yasha and Wrath Asura, Bonds might sound familiar to He who Howls and Rages from Naruto Shippuden: Ultimate Ninja Storm 2. Not only did Chikayo Fukuda compose both soundtracks, and CyberConnect2 made both games, but Bonds is even played during a fight in a wastelandish area similarly to He Who Howls and Rages.
In a way, his goals for trying to save the world are also very similar to Sigma, right down to being a former leader of the group of generals, being a Well-Intentioned Extremist, as well as having eye markings. To top it off, he's a mechanical humanoid that can feel, not unlike a reploid.
The main ships used by the Seven Deities are known as Septentrion.
Yasha Rider Kicks the Karma Fortress. It helps he wears a mask just like a Kamen Rider would.
In the DLC trailer, we see the head of the Brahmastra falling to earth incredibly similar to a scene from End of Evangelion specifically Giant Naked Rei's head falling down to earth after Shinji rejects Instrumentality.
Asura having a giant arm coming out of one his stumps in episode 11.5 is similar to the way stuff comes out of Naota's forehead in FLCL. It helps that the director of the episode was a key animation director for the series. The arm itself also acts like a giant glowing vector from Elfen Lied and it often expands in size similar to Akimichi Chouji. The arm also eventually becomes uncontrollable by Asura a lot like Tetsuo from AKIRA not being able to stop mutating and explodes just like the final scene from the movie version of AKIRA.
Both episodes 11.5 and 15.5 are basically seen as the anime equivalent of Dragon's Lair or Space Ace, via the usage of traditional animation with button inputs put in. It can also be seen as the modern equivalent of the Yarudora Franchise.
The Tower in Naraka that Asura is shown climbing on twice looks very similar to Korin's Tower, and Naraka with all the yellow clouds looks a lot like the otherworld from the same series.
During the final fight with Deus, Asura uses what looks like Killer Bee and A's Lariat move to knock him away.
Akuma and Dan also make an appearance in one of the DLC episode interludes, as does Chun Li. One of the images is also an exact copy of the iconic Street Fighter II intro.
Ryu cameos in the same interlude as a promotion for the Asura vs. Street Fighter DLC, which is likely why several Street Fighter Characters cameo in Some of the DLC interludes.
The entirety of episode 22 can be seen a massive Shout-Out to the final battle in Gurren Lagann. More specificly Lagann Hen.
The way the first half of the battle plays out is VERY similar to the first phase of the Cubia boss in .hack//G.U., and Asura's Destructor form even has wing fins that look similar to Haseo's Skieth The Third. There's also a lot of similarities to series like Gunbuster/Diebuster, as well as Heroic Age seen throughout the battle.
Some have spotted that the attack patterns of the boss is similar to the attack patterns of Mundus in his own first phase in Devil May Cry 1.
The Event Horizon stage by itself before the fight with Chakravartin the Creator. is very similar to the final boss fight stage, the Demon Tribe's World of The Legend of Zelda: Skyward Sword against Demise, only with a bright sunlight instead of stormy skies.
The atmosphere and stage of the Chakravartin the Creator fight is similar to the final Xemnas fight from Kingdom Hearts II. The music, another remix of In YourBelief, is composed similarly to Kingdom Hearts music as well.
The final fist fight is very similar to the The Fist fight Simon and the Anti-spiral have in Gurren Lagann: Lagann-hen.
Chakravartin's Creator form's body shape and structure is very similar to Seth from Street Fighter IV. He also is very similar to a color inverted version of The Anti Spiral.
Asura sacrificing his own life to save the planet from it's suffering caused by Chakravartin by disappearing into light is very similar to Madoka's own sacrifice from Puella Magi Madoka Magica. The reason for his death is also similar to how Nia dies in Tengen Toppa Gurren Lagann.
In the Episode 22 ending, Mithra resembles Maya Fey in appearance.
In the Lost Episode 1, Asura's QTE counter to Ryu's Tatsumaki Senpuukyaku is parrying it ala Street Fighter III and then countering with his own. He also uses a Kinniku Buster to Evil Ryu's groin.
In the Finale of Lost Episode 2, Oni and Mantra Asura get into a Pummel Duel not unlike the pummel duels seen in God Hand. The entire finale of the fight is similar to a fight right out of Dragon Ball Z.
The stage used for Lost Episode 1 is a reference is Sagat's stage in Street Fighter II, with a Taison replacing the buddha. It even starts off with a remix of his character theme.
Asura using Augus's blade while it's clenched in his teeth is a reference to Zoro from One Piece, but doing it armless is also a reference to Raiden in Metal Gear Solid 4, who did the same thing when killing Vamp (Asura even kills Augus in the same manner Raiden killed Vamp). His rampage against the Gohma with just the blade in episode 11.5 is similar to Zabuza tearing through bandits to kill Gato in Naruto.
During the first Deus fight, Yasha punching his energy straight through Asura to attack Deus without hurting Asura is a reference to Jojos Bizarre Adventure. Considering that Hiroshi Matsuyama in a recent interview for his new Jojo's Bizarre Adventure game states to be one of the biggest fans of the series in existence, it's not surprising.