One of the messages dispensed from the Fortune Teller is "Your princess is in another castle".
Collecting enough mushrooms in Afterbirth turns you into a mushroom-person, strikingly similar to a Toad.
Repentance adds the Mega Mush, and just like the Mega Mushroom, it turns Isaac gigantic and allows him to defeat nearly every enemy just by running into them.
The game's logo is very reminiscent of the first game's. The Japanese logo for Rebirth is instead a parody of the logo for The Legend of Zelda: A Link to the Past, with a pentagram replacing the Tri-Force.
In Rebirth, alternate trapdoors can send you to underground rooms that are just as blatant.
Many enemies are also reminiscent of Zelda enemies. The most noticeable are the Chargers (which behave like Ropes), Knights (which behave like Darknuts), and Pokys (which behave like Traps).
Rebirth added Mom's Hands (which behave like Wallmasters) and Bonies (which behave like Stalfos).
Teleportation items may randomly send you to a room with a guy saying "I AM ERROR."
The Stepladder from the original Zelda's functionally identical counter-part, simply called "The Ladder."
Chub can be made to eat bombs to damage her, just like the Dodongo. Rebirth even adds a "Chub dislikes smoke!" line.
Afterbirth adds a new challenge called "I Rule!", which gives you the starting items of a sword, a shield, the Ladder, and the Boomerang.
Afterbirth+ added a fairy that flies towards tinted rocks, entrances to hidden rooms, and rocks hiding trapdoors. The name? YO LISTEN!
Repentance adds the Spirit Sword, which gives Isaac a sword he can swing in front of himself. By holding down fire and then releasing, it unleashes a spin attack, and when Isaac is at full health, it throws out a Sword Beam, much like how the Master Sword typically does. To drive the point further, you unlock it by completing the Isaac's Awakening challenge, which starts you off with the Spirit Sword, the Trinity Shield, and Mom's Bracelet, which functions similarly to the Power Bracelet. The challenge ends with the fight against Mother, who has a Tennis Boss attack just like endgame Zelda bosses usually do.
The Empress card normally transforms you into the same demon Eve becomes. In Repentance, the reverse Empress card instead turns you into Magdalene, with the message "The morning sun has vanquished the horrible night."
The Holy Water subweapon is available as a Familiar, and functions similarly to its Castlevania counterpart, leaving behind a puddle that will damage enemies. Repentance buffed it to be even more like the original, since it's now thrown at enemies rather than shattering when Isaac takes damage. It even has unique synergies with both BFFS! and Fire Mind, which both cause the Holy Water to leave behind a blue fire, completing the reference.
The Mask of Infamy bears an intentional resemblance to the recurring boss Carmilla.
One of the endings: Isaac dresses as Dr. Fetus from Super Meat Boy, complete with the stage title theme from that game. Unsurprisingly, the ending gives you the Fetus in a Jar powerup. There's also a power-up called "Doctor's Remote," which is another reference to the character in question.
C.H.A.D. can appear as an alternate version of Chub.
Meat Boy himself appears as a familiar when you collect Cubes of Meat, and Wrath of the Lamb adds a "SMB Super Fan" circular saw item that transforms the player character into a Meat Boy lookalike.
The Larry Jr. boss is presumably related in some way to Larries' Lament from the second-to-last world of Super Meat Boy — possibly meant to be the miniature versions of them that pop out of their head in the ending.
Rebirth has Bandage Girl appear as a familiar when you collect balls of bandages.
A more meta one: the achievements for completing floors without getting hit in this game follow a scheme of "____ Boy", which is the same pattern that the achievements for completing worlds without dying in Super Meat Boy followed.
One of the new bosses introduced in Afterbirth is Little Horn, not to be confused with Super Meat Boy'sLittle Horn.
One of the Devil Room items in the original game is "Lord of the Pit", which turns Isaac into a black-winged demon similar to the one depicted on the card.
One of the powerups you can get from the Devil Room in Wrath of the Lamb is "Spirit of the Night", which changes Isaac's face to look like the card of the same name.
The Beginner Deck item in Rebirth is a reference to pre-built decks, and it tattoos the "color pie" on Isaac's forehead whenever you take it.
Rebirth also adds the iconic "Black Lotus" and to the list of items you can get. Fittingly, it's one of the rarest items in the game and has a strong and generically useful effect.
Also from Rebirth, we have the Chaos Card, which is a reference to the infamous Chaos Orb.
Afterbirth+ adds three more unlockable cards: Era Walk, based on Time Walk, Ancient Recall, based on Ancestral Recall, and Huge Growth, based on Giant Growth. These cards and Chaos Card also appear as a pixelated MtG card back when on the ground.
The Spindown Dice added in Repentance references the D20s used to track your life total in MtG.
Booster Pack is a card counterpart to Mom's Coin Purse, dropping five random cards on pickup. Its appearance is specifically a Magic: The Gathering pack.
There are multiple references to the classic "Gotta catch 'em all" slogan, such as the Meat Cube's flavor text reading "Gotta meat em all" or the Jar of Flies' flavor text reading "Gotta catch 'em all?". The aforementioned Friendly Ball and Poke Go naturally also reference it with "Gotta fetch em all!" and "Gotta catch em..." respectively.
One of the new items in Wrath of the Lamb is the Notched Axe, a pickaxe that can be used to break rocks. This is a reference to Minecraft and its creator, Notch. In Repentance, the item was reworked to work on a durability system that functions exactly like a Minecraft pickaxe.
Both Book of Virtues and the Judas Birthright Book of Belial grant Notched Pickaxe Minecraft-themed improvements. Virtues causes it mine coal, iron, gold, redstone, and diamond-themed wisps from rocks, which have effects based on their Minecraft equivalents. Belial gives Notched Axe a variety of bonus effects based on enhancements (increased durability (Unbreaking), faster attack speed (Efficiency), increased knockback (Knockback), burn damage (Fire Aspect), and more pickups from destroyed objects (Fortune)), including the purple glow overlay graphic that Minecraft uses.
There's an Afterbirth item called Mine Crafter, which summons a TNT barrel (updated in Repentance to a TNT cube).
The Wrath boss is basically Bomberman. In addition, players will occasionally find a room styled after the mazes from Bomberman's multiplayer filled with bombs to collect.
Adding to this, the Afterbirth expansion adds the item Bomber Boy, which makes bombs explode in the Bomberman cross fashion. It even gives Isaac the little antenna that Bomberman uses on his helmet.
A number of internet meme faces make an appearance, particularly the Forever Alone and Troll Face, with the latter appearing on bombs which are ready to go off. And let's not forget Shoop-Da-Woop!, which is a charged laser weapon. There is also an enemy type with a distinctive trollface that will split in half upon receiving enough damage, and the duplicates will split further into even smaller copies, demonstrating the spirit, as well as appearance of the trollface. In its smallest form, it becomes a Pokerface. Occasionally, the corpse sitting in one of the secret rooms will be sporting the "forever alone" face as well.
One enemy type is the same species as Gish. Gish himself can appear as a boss as well, and drops a baby version of himself (a familiar whose shots slow enemies) when defeated.
Additionally, the Sisters Vis, the bosses of the third area in Gish, can appear as a boss in the Depths.
The floor Gehenna, an unlockable variant of Mausoleum, also draws visual inspiration from the 7 Planes of Hehenna, the chapter in Gish where the Vis Sisters were originally fought.
The "Pills Here!" message after picking up a pill is a shout out to Left 4 Dead.
One effect that pills can give you is "Balls Of Steel," which gives you 2 soul hearts.
The null effect for pills is "I found pills!", with the fake effect "And ate them". This is likely a throwback to an early LOLCat macro. The Horse Pill version makes Isaac's face resemble the "HURRR I'M A HOERS" meme.
The "My Little Unicorn" item seems to be a shout out to My Little Pony.
The "Technology" upgrade is a clear reference to the Borg.
One of the messages you can get from the Fortune Teller is "Look to La Luna." This was the clue on how to find Reptile in the original Mortal Kombat (1992) game. Two others, "MARRY AND REPRODUCE" and "STAY ASLEEP", reference They Live!. It's also possible to get "I feel asleep!!"
The Necronomicon's cover (which looks like a distorted or disfigured face) is the same as in Evil Dead.
The Wire Hanger item is a reference to the film Mommie Dearest, in which an abusive mother screeches the famous quote: "No more wire hangers ever!"
One of the new items in Binding of Isaac: Rebirth is the Ludovico Technique, which leaves Isaac's eyelids pulled back, as in the classic scene of Alex's reprogramming.
One of the items is a magnet that attracts consumables to your position. Its name? Magneto.
The Dople (a skinless Isaac's doppelganger in The Womb) is a reference to Tomb Raider I, where a skinless enemy who mirrored Lara's movements had to be killed by being lured into a lava trap, similar to how Doples can be lured into spikes.
Two new pill effects in Rebirth are "Lemon Party" (a reference to an infamous Shock Site) and "R U A WIZARD". (Lemon Party drops a very large, very damaging Lemon Mishap puddle, while R U A WIZARD gives Isaac temporary Fish Eyes that force him to fire each shot at a 45 degree angle instead of straight ahead.)
There's a little nod to a certain meme started/nourished by Northernlion. "Rebirth Got Canceled" is one of the new Fortune Teller message, which was a popular joke statement back before the game's release, and a thinly-veiled Take That! towards Phil Fish, who decided to cancel Fez 2 after a particularly bad meltdown.
One of the card items in Rebirth is A Card Against Humanity. It fills the room with poop when you use it, referencing how the first Card Czar is chosen in the game's rules (whoever pooped last goes first).
Crack The Sky is a reference to King Lear, but also to an album of the same name by Mastodon.
Two new pills added in Afterbirth are "One Makes You Larger" and "One Makes You Small", referencing the Jefferson Airplane song "White Rabbit". Presumably they'll still work if you get them from Mom's Coin Purse/Mom's Bottle of Pills, though.
Afterbirth added an item called Black Powder which lets you draw circles of the eponymous substance to form pentagrams that deal damage to enemies standing in the area, with the description "Spin the black circle." (The song itself being about the singer's preference for vinyl records.)
Spider Mod is a reference to Spidermod, an extensive Game Mod for the original The Binding of Isaac. Its creator, Spider853, was a lead developer for Rebirth.
The description for one of the new items in Afterbirth, the Lil' Chest, reads "What's in the box?"
The Forget Me Now item is a reference to Arrested Development. On the show, Gob the magician gives people who figure out one of his tricks a "forget-me-now", which is a roofie.
The icon of one new item in Afterbirth, Zodiac, is very similar to the symbol the serial killer known as the Zodiac killer used to sign his taunting letters to the police and press.
There are 3 very hard to unlock items called The Body, The Mind, and The Soul. Their descriptions are respectively "I feel all", "I know all", and "I am all". They are a reference to the movie Highlander, as the three are said almost verbatim when MacLeod wins The Prize.
The pickup quote "Game breaking bug, right away!" is a reference to a quote by Phil Fish in Indie Game: The Movie, where he says the exact same words when a bug is discovered in FEZ on the first day it is being shown at PAX. This has been confirmed by Edmund himself on twitter.
The description of the Louse (a trinket) reads: "Itchy. Tasty..."
You can get a potato peeler that permanently raises your damage and gives a meat cube for the entire run. The price? A pound of flesh.Repentance also adds an item literally named "A Pound of Flesh" that causes shop items to cost health instead of money and Devil deals to cost money instead of health.
One of the items introduced in ''Afterbirth+" looks exactly like the classic Butter Bean, but is actually a unique item called Wait What?. The flavor text for this item states that "I can't believe it's not Butter Bean!"
The first booster pack for Afterbirth+ saw the addition of Bozo, an item that paints Isaac as a Sad Clown. This item is, of course, a reference to Bozo the Clown, a popular TV character during the 60's and 70's.
A new item added in the second booster pack for Afterbirth+ is Leprosy. Its tagline? "You're tearing me apart!"
The Telekinesis item in Booster Pack #2 allows Isaac to hold enemy shots in place. The icon shows a hand with an open palm and the thumb tucked in, exactly like Neo.
Booster Pack #3 features a new angel room item in the form of a prism. Its pickup quote is "Eclipsed by the moon".
Booster Pack #3 also features a new shop item called Mr. ME!, which spawns a Captain Ersatz of a Mr. Meeseeks to perform a task for the player. It's based in part on a workshop item that summons the genuine article.
Booster Pack #3 also added the Door Stop trinket. Its tagline is "Hold the door!"
One of the Steam Workshop items added in Booster Pack #5 (also known as The Forgotten update) is a familiar version of Spewer.
Booster Pack #5 locks certain bosses behind two achievements that require defeating ??? with 3 and 6 characters. The achievements for completing this are called "Something wicked this way comes!" and "Something wicked this way comes+!", after the famous line from the Witches.
Repentance adds a spinning top item called Spin to Win. Its pickup quote is "Let it rip!".
Repentance allows you to input SVPE RH0T in the seed menu to unlock "Super Hot mode", which significantly slows down everything if Isaac isn't moving.
In Repentance, you can kill the otherwise impervious boss Great Gideon with the Chaos card, which spawns a unique crawl space that contains two items, two chests, and a key. The crawl space is named Gideon's Grave in the game's code, referencing both the main antagonist of Scott Pilgrim and his Chaos Theatre.
King Baby's description used to be "Lord of the dead". Repentance changed it to "Hail to theKing Baby!".
Similarly, Freezer Baby has the pickup quote "Iced Iced Baby".
Decap Attack, both in name and function, is a a shout-out to the Sega Genesis game of the same name, which revolves around a character who throws his head to attack.
, not to be confused with Super Meat Boy's Little Horn