3D Dot Game Heroes/Shout Out

As Three D Dot Game Heroes is an unapologetic love letter to The Legend of Zelda and other games from the 8-bit era, it's only natural that a game like this one is Shout-Out and Reference Overdosed.

Demons Souls

 * One of the girls in Dotnia Castle will offer to trade you for "some demons game" because she thinks it's too hard.
 * There is also a Developer's Room cave where you can find a message saying "Help! I'm in trouble! Please recommend this message!" which says that if you recommend it then a person gets healed, as well as some Sticky White Stuff and a dead body containing a Hero's Soul.

Metal Wolf Chaos

 * Before the King sends you on your way to the final dungeon, he says that he has the utmost confidence in you. Why? Because he's "THE GREAT KING OF DOTNIA KINGDOM! YEAAAAAAAH!!"
 * The Metal Wolf exists as a selectable man-sized character model.

Otogi

 * Raikoh has his own character model.

Tenchu

 * Rikimaru, Ayame, Rin and Dr. Tesshu have their own character models.

Armored Core

 * The White Glint from Armored Core: For Answer has its own character model.
 * A patron at the inn in Raejack village thinks a 3D mech game would be awesome (and so do two of the developers from the aforementioned "From Cave").

Kenka Bancho

 * One of the character models is a long-haired Bancho.

General

 * Take a look at the loading screens, and you'll see that they're all modeled after video game box art. Some that come to mind immediately are Castlevania, Mega Man, Final Fantasy V, The Tower of Druaga...

Bionic Commando

 * One of the castle guards tells you "We've located Superb Joe! Head to Area 07 and save him!"

Castlevania

 * When you take Ice Candy from one of the Dotnia Castle guards during the endgame, you get the message "You now prosess Ice Candy" as a reference to a recurring grammatical error in Castlevania II: Simon's Quest.

Dragon Quest

 * You'll meet a fortuneteller/dancer sister duo named Mina and Mary (Meena and Maya from Dragon Quest IV).
 * In Raejack Village, one house contains a guy who's trying to choose between marrying his childhood friend and a rich girl he thinks has a better spell list (Dragon Quest V has a plot that revolves around this). For bonus points, he uses the same rationale for each possibility that Konata from Lucky Star used in reference to this decision.
 * Also in Raejack is a slime named Bluesy who wants To Become Human (reference to Healie/Doc the healsime from Dragon Quest IV, who later actually does become human).

Final Fantasy

 * Raejack Village has an inventor named Dr. Dic ("Cid" spelled backwards).
 * He has a grandson named "Dim" who talks about summoning "Deathtax".
 * This could also be a double reference to Soul Blazer. Which involves summoning a demon called Deathtoll.
 * There is also a kid who teaches you a "magic spell": "Pam nepo ot 1L sserp!" This is a nod to the brooms in Matoya's Cave in the first Final Fantasy I, whose backwards talk shows you how to access the world map.
 * One of Sir Signe's signs reads "D3 si dlroW ehT," a nod to a message in Daryl's Tomb.

Gauntlet

 * Examining a corpse in the 4th dungeon reveals a message that says "Hero needs food badly."

Kings Knight

 * The first village near Dotnia Castle is called Raejack, a possible reference to Rayjack the knight.

The Legend of Zelda

 * For starters, the game itself.
 * Right at the start of the game, when the king gives you your first sword, he will tell you "It's dangerous to go alone! Take this."
 * Be careful when attacking chickens with your swords. Eventually a bunch of them will come out of nowhere and peck you to death.
 * Lee, the fairy you meet after recovering the Ancient Sword, serves as your Exposition Fairy, similar to (but only a fraction as obnoxious as) Navi from The Legend of Zelda Ocarina of Time.
 * A man in Raejack Village, after paying him 30 G for advice, will start to say "Eastmost penninsula [sic] is the secret", but changes his mind.
 * The "Forest of No Return", which houses the second temple.

Mega Man

 * When you acquire the Dash Boots from Dr. Dic, he says "MESSAGE FROM Dr. DIC! DASH-BOOTS COMPLETED! GET YOUR WEAPONS READY!". (Apparently, he's always wanted to say that.) This is a reference to Dr. Light's Item Get message from Mega Man 2.

Metroid

 * One of the random pieces of advice given by a Raejack villager is "Apples don't explode, so bomb jumping is useless". Bomb jumping is a staple of the Metroid series, as it helps Samus get around really tough areas.

Spelunker

 * Enter your name as "Spelunker" when creating a character, or rescue him on the northwest corner of the world map to enable Spelunker mode, where one hit from anything hazardous kills you instantly.

Wizardry

 * There's an inn near the forest temple called Wardna's Inn, which looks a lot like Werdna, the boss of the first few Wizardry games.

Ys

 * A message from a dead soldier refers to how even running into enemies from the side was useless.

Jaws

 * You can have a shark as you character model, whose flavor text reads "You're gonna need a bigger sword. He bites!"

Neon Genesis Evangelion

 * When you collect the Gold Ring, the game states the effect that causes your damage to be reduced is called an "Abnormous Terror Field".