There are a couple of Golden SunShout-Outs throughout the series: the Heaven's Gate sword bears a striking resembance to the Titan Blade, Water of Life appears as an item in the first two games, and Seiken is similar to the Ragnarok unleash, not to mention the actual Ragnarok Limit Break from the third game, which takes the same "summon a magic sword to fall on an enemy" idea up to eleven.
The final boss , a neo-Nazi named Lance and his tank, seems to be a blatant Shout Out to Valkyrie. The tank's pilot even wears an eyepatch like Tom Cruise's character does in the movie; but actually, the tank was inspired by Metal Slug; Matt called it the Valkyrie because some friends of his noticed that Lance looked like Tom Cruise's character, which surprised him because he hadn't seen the movie.
There's an NPC early on wearing Kamina shades. Later, the man himself appears, alongside Simon and Yoko, who all give you quests. Kamina will even teach your characters the "Tera Drill".
Using Tera Drill the first time will prompt the user to say "Pierce the heavens with your drill!" The old flying robots with drills seen in the second game are now described with something like "They'll pierce your heavens.", and when they use a drill attack the first time, a character will remark that it's a good thing they don't have the spirit for a Giga Drill Breaker. Yup, lots of Gurren Lagann Shout Outs...
Yoko's quest nets you the Flame Skirt, armor for Natalie that is exactly the same as Yoko's outfit, and has high fire resistance.
Yoko's hairpin can be found in the secret area of Kitten Ruins, which increases accuracy. Simon's quest also gives you a pair of drill hairclips, which increase defense.
Konata is a NPC who gives you a quest, and if you complete it, she rewards you with chocolate cornets. Also, one of Natalie's spells is called "Lucky Star", though that may be just a coincidence.
The NPC for the first minigame is a samurai with an odd manner of speaking named Sir Ken.
And the NPC for the final minigame is Curly. When you speak to her the first time, her first sentence is actually "Did you know the witch woman Jenka had... oh, wrong person.", which is another reference to Cave Story. She also describes the minigame as "Looks like your cat wants to speedrun this stage", which could be a reference to how many players speedrun the bonus level in Cave Story.
Matt's Protect move summons a slightly modified Triforce.
The Final Boss, Akron, has an attack that turns the screen black with eyes and jagged smiles, which is reminiscent of Pride from Fullmetal Alchemist or Alucard's transformations.
The Power Metal attack plays a few notes from "Through the Fire and Flames", named outright by the characters when used.
When a character gets hit in the third, sometimes they have the "shoop da whoop" face. invoked
Fighting a Trojan Horse enemy in the first area and witnessing it use its buff ability will cause the player characters to shout, "Its the Horn of Gondor! It boosts their morale!"
The Cosmic Monolith is an obvious reference to 2001: A Space Odyssey.
When the Ancient Monolith in the fourth area unleashes its beam attack, Matt will say "I once knew a guy with golden hair who shot beams like that. Was nasty."
Lance also implies in an early conversation that he stole his scouter from Vegeta.
Bill: That's an interesting device you've got there, my son.
Lance: I'm not your son, and it's called a scouter. I stole it from a guy with a rough attitude and a tail. It seems to gauge an opponent's power level.
When fighting a Fire Elemental for the first time, Lance may comment about how it must think it's a Mobile Suit, with the beam sword and all.
The bonus version of the third boss is essentially Utsuho, complete with a near-replica of her Mega Flare spellcard.
The second Bonus Boss cribs off of Flandre, specifically her Cranberry Trap and her And Then There Will Be None? cards, as well as ganking Yukari's Border of Wave and Particle.
Lance's bomb is his giant laser attack, which works remarkably like a Master Spark here.
