For a flash game tetralogy with two Gaiden Games, Epic Battle Fantasy has a lot of Shout Outs. With the third game's open world exploration that continued on to the 4th, the games started to pick up greatly with more references.
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.
A small clip of DragonForce 's Through The Fire and Flames plays when Matt casts "Power Metal".
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. 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.
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 LagannShout Outs...
Yoko's quest nets you the Flame Skirt, armor for Natalie that is almost 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 nets you a pair of drill hairclips, which increase defense.
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." 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.
Wild ARMs 2: There's a battle robot named Jack, and Lance's Heavy Claw weapon looks like the weapon wielded by Ptolomea.
An NPC that offers a quest for mushrooms says "Mah boi!"
The victory fanfare bears a strong resemblance to that from the Final Fantasy series.
The use of the '3.3' rather than something like 3.5 or 'gaiden' is probably a Shout Out to Touhou, which has Hisoutensoku as 12.3note This turned out pretty well, since there ended up being two other spinoffs that took 12.5 and 12.8, but it looked damn odd when it was the only one.
More than one Minecraft references have been made during the game. As the party meets a miner who advises them to "never dig straight up or down", which makes Lance reminisce of a mining trip that was ruined by spiders and exploding monsters. Examine the snow sculpture of a Creeper in Whitefall with Lance in the first slot, and he has a Heroic BSOD.