Considering how 3D 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 chock full of Shout Outs at every opportunity.
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.
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.
For the Dragon Quest series in general, you'll occasionally see fast-moving "Crystal Slime" enemies. If you can corner one and kill it, you'll get a good monetary reward.
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 the healslime from Dragon Quest IV, who later actually does become human). Subverted near the end of the game when you use the Mirror of Truth on Bluesy, and he changes back into a slime.
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, 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.
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 mid-sentence.
The "Forest of No Return", which houses the second temple. One wrong turn and you're warped straight back to its entrance.
Bomb open caves and you may encounter Gobins who give you money (which, of course, "is a secret to everyone") ... or cranky old men who complain about it and take some money for repairing the "door" to their house.
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.
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.
Among the various user-created character sprites included in the game is "Robo Team": A Hero-class sprite of four tiny vehicles that combine into a sprite-sized robot, and apparently debate "who will form the head" from time to time.