If you go on a sightseeing date with Ayano, she attacks a pigeon and says that pigeons freak her out because she thinks they can take over the world someday... which is exactly what they do in another game that pokes fun at many dating sim tropes. Pamu also has a line of dialogue at Friendzoned level about wishing that she was in a better game, like "that game with pigeons".
One of Pamu's early generic messages (mis)quotes Rick and Morty. Her line "Wabba lubba dub dub!" is the catchphrase of Rick Sanchez in Rick and Morty, except misspelled as "Wubba lubba dub dub" (though this was eventually fixed).
Cassie, with her hair decs and twin tails looks a bit like Usagi Tsukino.
But it's Pamu the Magical Girl who asks if you'd mind donning a tuxedo, a mask, and a top hat during sex.
Iro's appearance and attitude, as well as some of her quotes (such as saying she feels like she belongs in the sky) make her seem like a perfectly humanized version of Rainbow Dash.
Ayano: It's kind of sad that Iro is such a blatant rip-off of another character. All of her appeal has nothing to do with her.
Many of the job level titles and their achievement descriptions are shout-outs to pop culture. Examples include "The One" and "Chiroptera Hominin" (a Latin phrase that means "bat man"), the last two levels of Hunting.
The enchanted jam is probably a reference to the jam from Kanon.
Pamu references the old YouTube meme of Dr. Robotnik saying "Pingas". Or rather, it's slightly less well known cousin Hap-Piness.
Qpernikiss sings the first line of the Attack on Titan intro in one of her greeting lines.
In the German, Italian and Portuguese translations of the game Cassie calls you Scrooge McDucknoteor rather his name in those languages after you pay for her bills.
Mio: What makes a woman turn neutral? Lust for gold? Power? Or was she just born with a heart full of neutrality? Nutaku: I find the most erotic part of the woman is the boobies.
In her phone fling, Mur asks for suggestions on the title of her upcoming hentai harem manga. You can offer such names as Honey Love Pot and Heartful Girlfriends.
Mio
At higher relationship levels, Mio can mention buying gun heels.
While referring to Samus Aran, Mio claims that she probably "bangs like a tiger"—an infamous line from a fan-made Tales of Phantasia translation.
The Summer 2017 event featured, as a reward, a bonus swimsuit for Mio modeled on fellow Gamer ChickD. Va. She also implies she's a Winston-main.
At the Sweetheart level, in reference to Alice's Adventures in Wonderland and its sequel Through the Looking Glass, she's got the Tea Set as one of the gift requirements (referring to the Hatter's tea party in the first book), and the selection quote is "Oh frabjous day! I was hoping to see you!" — 'frabjous' was a word invented by the author of the books, Lewis Carroll, and first used in Through the Looking Glass.
You can occasionally catch her "out of character" singing the song "Bubbles and Birds", just as you can catch resident sex symbol Moxxi singing the same song in Borderlands: The Pre-Sequel!.
Being a personification of the porn site of the same name, Nutaku, she supposed to normally plugs other games available on the site. And in one case, she does that by indirectly name-dropping another game that was previously hosted there.
Luna seems to be a reference to Lina Inverse from Slayers.
The title for her Lover level is "More like Shabranig do me", referencing Shabranigdo.
Eva
In Eva's introduction cutscene, you crush her mecha, and the narration helpfully suggests that you dramatically save her, and 'try not to fall on her hands-first'. This is referring to a scene in Evangelion where Shinji does exactly that, falling hands-first on a naked Rei and accidentally groping her breasts in the process.
The Lance of Longinus can be seen floating in the sky when you take Eva on a Moonlight Stroll.
In an Awkward Besties Flirt, Eva will tell you that she's met Cassie, and that she reminds her of a colleague of hers, and would make an excellent pilot. She's referring, of course, to the Queen of all Tsunderes, Asuka Langley Soryuu:
Eva: I met your friend Cassie. She reminds me of a colleague of mine. She would make an excellent pilot.
Darya has a couple of references to Steven Universe. Fitting, since her schtick revolves around diamonds.
She mentions that her physical form is made of hard light, which is also what the bodies of the gems are made of.
Conquering planets and taking their resources for her home sounds an awful lot like what the Diamond Authority does with their planet colonies...
In one of her midlevel dialogues, she mentions that her people have a process called "synthesis," in which two become one. Fusion, anyone?
She asks if the protagonist has encountered any rebellions.
When you reach Lover level, she says her love for the protagonist shall transcend time, space, and choppy release schedules.
She compares herself to a pink diamond and says that she's made of love in high-level dialogues.
Shibuki
Shibuki gleefully chops up the fruit during a beach date, claiming that she always was a serious Fruit Ninja.
Peanut
Peanut's character design is loosely based on the Lofi Study Girl, she has the same hair style, also dressed in orange and green/blue, and one of her pinups is of her copying the famous lofi girl pose, studying at her desk with an orange cat in the background (though she doesn't appear to be left-handed)
Renée
Multiple from Renée, plenty of which are references to books:
Renée: Remember when we found that abandoned treehouse in the woods? We used to swing across the creek on a rope, and pretend we were crossing into a magical fantasy world. But then the rope broke, and... We grew up.
Attempting to give Brie a gift in the early stages of the relationship has her remark that she feels awkward and embarrassed, and then go "Woop woop woop woop woop!"
After the issue with the non-Cheesy Moon is cleared up and Brie learns that there's cheese on Earth, she apologizes for not properly greeting Marshmallow earlier and says "Na-nu na-nu!"
When she asks Marshmallow to help her experience the various cheeses of Earth, she initially phrases it as "Help me, Earthling... You're my only hope," before apologizing if she sounded too serious.
One of her responses in later relationship levels is a shout-out to Lilo & Stitch:
Brie: Do you want to see a picture of my dog? Well, actually, he's a genetically modified experiment designed to cause intergalactic chaos and destruction, but he's kind of like a dog. Either way, he's family, and I love him!
Brie can tell Marshmallow that, in the event that hostile aliens ever invade the planet, to just remember: "Never give up. Never surrender!"
Upon unlocking and switching to Brie's Naked outfit in the 18+ version, she'll state "Your clothes. Give them to me. Now. I'm not going to wear them, I just want us both to be naked!"
One of the "Talk" dialogues is Nightingale picking up a knife because of its shine and Marshmallow ordering her to drop it while calling her an entitled goose.
One chat has her provoking Marshmallow into chasing her around for fun by going "Meep meep!"
.