The Japanese version's chapter titles for when Gemini, Erica, Ohgami and Sakura joins up references which game they debuted in their series's.
Stage 6 is titled "The Banner of Love on the Skyscrapers", where "The Banner of Love" was SW3's opening song ("Ai no Mihata") and where Erica first debuts; the "skyscrapers" refers to one of Gemini's lines "To the rooftops... Bang!".
Stage 9's "To Scatter Evil, To Exemplify Justice" is a line from the first game's original opening song "Geki! Teikoku Kagekidan".
Stage 15 actually takes place in the setting of the old Sega action-strategy game Gain Ground. In fact, the supercomputer from said game can be seen before the stage begins. Stage 17 is based off Gain Ground's first boss stage.
Speaking of old Sega games, Stage 17's "Operation Crackdown" is a reference to the game Crack Down, where you play as agents planting explosives.
In Dante & Demitri's post battle conversation with Lindow, Dante mentions Lindow's right arm would be good for throwing demons, something Nero from DMC 4 could do; who coincidentally has an arm kind of like Lindow's.
Sänger's post-battle conversation involves Dante suggesting Sänger that he should become a hunter, with him replying that he likes the sound of "The Sword That Smites Demons". Demitri replies that he knows another hunter with a ridiculous-looking sword, referring to Donovan.
When Jin and Xiaoyu rejoin the party, Jin and Heihachi try to kill each other. Xiaoyu says, "Why, Jin? So much blood! So much vengeance!"
Alisa calls Jin a refrigerator, Xiaoyu then corrects her calling him a warm refrigerator, Jin has no idea what they're talking about: this is another reference to Blood Vengeance.
When Rikiya Busujima reappears, he ends up outside a zombie-infested mansion. He tells Jill and Chris to be careful, because it's The House of the Dead. Followed immediately by the chapter title which reads exactly what he just said.
Rikiya gets taunted by Lord Raptor when he's warned to prepare for zombie revenge.
Ryu and Ken's left+A attack is directly taken from the final fight with Bison in the Street Fighter II animated movie.
Their Shotoclone status is pretty much brought up in the game as well. Winning with Batsu as their Solo Unit will make him utter the victory quote he used in Tatsunoko vs. Capcom regarding their fighting style being similar to Shimazu Karate* This is a reference to Hideo Shimazu of the Rival Schools series who plays similarly to Ryu. Starting a fight with Ulala as their Solo Unit will make her interview Ken while pointing at Ryu, causing Ken to wonder why he and friend are always being mixed up.
If Akira and Pai get paired up with Rikiya, the latter warns the former not to use martial arts that might shoot out ki energy. This is also another reference to the Shotoclone status of Akira in the Virtua Fighter series since he only uses attacks that don't involve the expending of ki energy.
Pair up Valkyrie with Riela, and the former will advise the latter to "Use your gifts responsibly, it is the duty of people with great power." Just switch a few words around, and it's similar to the classic line delivered by Uncle Ben in Spider-Man.
Pair up Juri with Akira, and sometimes they will get into an argument about Tae Kwon Do. Pai, however, makes an offhand comment that she saw Juri shoot webs out of her legs.
Frank's use of the Double Lariat and the Flash Kick with Hsien-Ko is a reference to Zangief and to Charlie/Guile, the only Street Fighter characters (Not counting the EX characters) to execute the former and the latter.
In one chapter, the party ends up at the bottom of a fortress (The Tarqaron). Since they had to climb up a bit, Bruno remarks how he did not wish to scale a building ever again. Both Dante and Lady aren't too happy having to deal with tall buildings either in following chapters.
A weapon you can acquire over the course of the game is the "Divine Implements". It is described as a sword, bead and mirror set thought to be lost forever.
Chapter 11: Across Infinite Timenote The Japanese title actually makes a lot more sense, a close translation of "In the Land Exceeding Endless Time" - "Infinity at the Area Where it Exceeds" being the title of one of the tracks in Endless Frontier: Exceed.
Also with Heihachi, after a majority of the groups return to their home worlds, and the Portalstone is normal again, he mentions how he has no use for it and that the South Pole is looking more promising.
In Chapter 4, Reiji asks Chun-li how they arrived. After Chun-li's explanation, Xiaomu has this to say
The title of Chapter 34 "Is Paris Burning Again?" is a shoutout to the full title of Sakura Wars 3 with the official title "Sakura Wars 3: Is Paris Burning?".
It's also a real-life shoutout from the actual battle in the Liberation of Paris with the Allies (consisting of American troops, Free French troops and French guerrilla fighters alongside Spanish Republican exiles) against Nazi German-led forces (alongside Vichy Milice militia forces). During this time, Adolf Hilter supposedly asked military governor Dietrich von Choltitz if he followed his orders to raze Paris rather than allow it to be recaptured by Allied forces with the question "Is Paris Burning?"
Kill an enemy with Reiji, Xiaomu, and Saya and Saya may suggest that they team up and call themselves The Outfoxies: this is referring to an old obscure Namco arcade game that basically boils down to "Super Smash Bros. with guns".
During Chapter 16, Xiaomu also claims how she's one of Shinra's top "ghost chasers", likewise referring to a Japan-only SNES Banpresto game with the same name.
At the end of the Ghosts And Goblins level, Arthur holds the key to the huge gate they got from beating the Stehoneys and exclaims "Open up! I have a key for getting in!", a reference to the phrase mangled by Good Bad Translation in most of the games that pops up whenever you defeat a level boss.
After Juri gets tired of Seth and tells him she's gonna send his ass down to hell, Xiaomu agrees and tells him to say hi to cyberdemons when he gets there.
During the Chapter 5 intro, Xiaomu misremembers Kogoro's name as Mani Karabera.
There's one scene in Chapter 16 where it's an all out Nobuyuki Hiyamashouting at himself - the yellow goblins suddenly appear, and they're all voiced by Hiyama. They are followed by a reaction from Haken, Batsu and Demitri, all of who were voiced by the man as well, and Demitri even briefly lapses into goblintalk at the end of his line.
When Mii asks about how Batsu is doing with his studies, Batsu mentions that he isn't being aggressive enough. It's the direct quote of Hayato Nekketsu's victory quote in the Rival Schools series, and Hayato acts like Batsu's mentor. Of course, Kogoro doesn't know the context.
When paired up with Gemini and Erica, they mention the Party-Up Technique which is three characters teaming up with the enemy.
When paired up with Akira and Pai and winning, he will mention that he knows another friend named Akira who also does a similar kung fu style. Akira says that he'd like to fight her at some point, to which Pai replies that cheering him on might be difficult.
He also likes to reference voice acting gags - he says towards Zero that he can do Cyclone Twisters, which is Roy's Burning Vigor attack. Guess who is Roy's voice actor.
Similarly, Jin comments that Batsu should change his uniform, prompting Batsu to reply that he reminds him with his discipline school committee head named Kyosuke. Guess who is Kyosuke's voice actor.
Alisa's victory quote with X and Zero involves her wondering what the difference between Reploids and androids is. X thinks that Reploids can't take off their head and asks Zero if he agrees, to which he offers no comment, referring to Mega Man X2 where Zero spent most the game in pieces that X had to collect.
Bruno's intro quote with Jin and Xiaoyu involves Jin saying how there's lots of weird detectives around, to which Bruno comments he's heard of one who spends most of his time rolling around on the ground, referring to Lei Wulong from Tekken.
Bahn's victory quote with Haken and Kaguya involves Kaguya saying how Bahn's fighting style reminds her of someone she knows, referring to Aledy in Endless Frontier EXCEED.
Saya's intro quote with Kurt and Riela involves her commenting on their numbers and deciding she's Number 99, referring to the final boss in Namco × Capcom.
Pairing up Vashyron with Ryu and Ken will result in a conversation where the Ryu and Ken state that as an ex-solider, he should be launching Sonic Booms from his hands instead of using guns, referencing Guile from the Street Fighter series.
Similairly, pairing the two up with Imca will result in Ken saying that they can handle cars with their fists. Imca states that is impossible, but Ryu says it's rather common on their world. This alludes to the famous car-destroying minigame from Street Fighter II and Street Fighter IV.