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 resemblance 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".
Epic Battle Fantasy 1
The first game doesn't even bother with Shout Outs, and directly uses foreign material; the Pokémon Pichu, Mareep, Registeel, Regirock, Regice, The Golden Sun spell Catastrophe, the FLCL character Lord Canti, and Dragon Ball protagonist Goku are all present.
When you fight against the first robot, you can read "Mobile Suits" in the sign (it's a Gundam!). It also happens to be named Defender.
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. While the tank itself 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 third area has snow sculptures of Kirby and the Pokémon Pichu and Pikachu. The fourth area has a sand statue of Meowth.
Also in the third area: a snow sculpture of a castle and the Castle Crashers, and another snow sculpture of a White Mage, a Black Mage, a Fighter, and a Ninja using the character designs of Final Fantasy I. The heroes feel a sense of deja vu when both of these sculptures are approached, but can't quite put their finger on it.
Some of the electric slimes in the fourth area have Pikachu-style tails.
One of the attacks Leaf Eaters use involves sending razor sharp leaves at the players (a la the attack Razor Leaf from Pokémon).
One of the attacks the black crows use lowers accuracy. When this happens, Natz says "Pidgey used Sand Attack! Accuracy fell!".
DragonForce: The Diamond item is described as "The hardest metal known to man.".
The Game over screens for the third game always have a quote with some kind of Shout-Out:
Rurouni Kenshin: The NPC for the first minigame is a red-haired samurai with an odd manner of speaking named Sir Ken.
And the NPC for the final minigame is Curly from Cave Story. 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.
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.
There is a snowman of Balrog in the game. The differently toned eye lines are hard to see but there.
Banjo-Kazooie: You can use a honeycomb to increase your max life.
There is a character who looks like Ash Ketchum holding a stick in the beginning battle areas.
In the Beginning town of Greenwood there are boulders that can be moved by the player. moving them awards you the achievement "Used Strength"
You also get medals for using the axe, candle, and hammer for the first time, respectively named "Used Cut", "Used Flash", and "Used Rock Smash".
There is a man with a large sword called "Gust" with spiky light blond hair.
Fullmetal Alchemist: In the beginning town, there is a man named Alphonse with metal arms who identifies himself as an alchemist.
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.
Golden Sun: A mage named Mia who's used to the snow shows up in Whitefall.
Along with the numerous other snowmen, there are two Djinn outside a shop in the same village, a Mercury and Jupiter with the wrong color gems for eyes.