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.
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.
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.
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). 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.
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.
