All of the Seven Deadly Sins mini-bosses have an unique sprite not seen in any other enemy in the game... All of them, except Sloth, which is just a lazypalette swap of the Globins! That's a subtle, yet incredibly clever and ingenious joke.
Also, the worms he spawns that are usually pretty fast when charging are slower than the rest. They're lazy.
This has become even more plausible with the upgraded Sins from Wrath of the Lamb. Each has a disturbing new design... except Super Sloth, who's just a reskin of the Glazing Globins, as regular Sloth is to regular Globins.
Another of the Sins, Wrath, only attacks you with bombs. He can be damaged by these bombs, which doesn't seem to make a whole lot of sense...except that angry, or wrathful, people often do things that end up being self-destructive.
The familiar you get from obtaining the Cube of Meat can push your bombs around, which can often spell disaster for you. If you get three Cubes of Meat, he will get his own body and follow you around. However, he'll still push your bombs around. Getting the Fetus in a Jar item makes it so your only attack is bombs. It also gives you a top hat and a monocle, reminiscent of Dr. Fetus. Combining the resulting bomb-spam and Meat Boy will probably kill you, because Meat Boy will often push your own bombs back at you. Could this be Meat Boy trying to get revenge on Dr. Fetus?
Whore of Babylon transforms the character into a demon with high attack power, but only when you have only one heart — AKA when you are near death. ??? does not have regular hearts, ever, therefore having WoB always active. Makes sense, since he is a Dead Blue Baby, and therefore as close to death as possible.
Look at the names of the playable characters: Isaac (a sacrifice to God), Judas (a traitor), Cain (a murderer), Magdelene (a whore)note Mind you, that reputation is undeserved, but most people don't know otherwise, and Eve (the first sinner). Says a lot of what Mom thinks of her kids, doesn't it?
That says more about what Isaac thinks of himself, given that the other characters are Isaac in various costumes...
Another Fridge Brilliance moment comes in the addition of Samson, a man who was given incredible strength by God, and used it to great effect. It seems he's finally snapped out of his depression. The Wrath of the Lamb update in general showed that God has finally stepped into the ring to try and help Isaac escape.
Judas starts with 3 pennies, which seems odd — it'd seem more appropriate for Cain to have them, right? Except the original Judas sold out Jesus for thirty (3*10) coins.
It's more interesting than just "cancer makes you sad". The Cancer trinket has a unique effect in that it increases your rate of fire, without counting as a rate of fire upgrade. This means you can have upgraded your rate of fire to the cap, and Cancer will still increase your rate of fire, implying that no matter how sad you are, cancer can always make your situation worse.
Dad's Key allows you to exit any room, including challenge rooms. Now we know why Isaac only has a mom.
May fit under Fridge Horror, but ??? starts off with "the Poop." At first, I assumed this was purely because ??? is the Lethal Joke Character, so he starts out with the joke item. However, when someone dies, the muscles within their body relax, resulting in a post-mortem bowel evacuation. ??? starts out with Poop because that's actually all he had!
The Whore of Babylon is a curse effect when you drop to half a heart. When Eve ate the fruit and became the first sinner, she was cursed by God and cast out of paradise; this is why Eve in game has to carry this curse no matter what.
Envy has a distinctly trollface-like smile, and he also often drops troll bombs on death. Perhaps trolls are envious of what other people have?
All the trinkets you get from beating Blue Baby with a certain character is something they've lost! Isaac has metaphorically lost his head, Cain is missing an eye, Judas lost his tongue after his betrayal of Jesus Christ, Maggy has lost her faith, Eve's bird has lost its foot, Blue Baby has lost his soul, and Samson, in the Bible, had a lock of his hair cut off, which made him lose his strength!
Also, when you think about it, Isaac being a sacrifice for his mother means he's most likely thinking about being killed by his mother, and thus decapitation. Also, the head joins you like other, dead or imaginary, familiars.
This is continued with the items you get for beating the Lamb in Rebirth, where these items were moved. Azazel's unlock, though, doesn't make any sense. This is because this is unlocked through the Sheol path. However, if you beat ??? as him, you get Abbadon, which is a representation of the entrance to hell. So, if you take the Cathedral path, Azazel has lost his way home. Isaac's item was changed to the Missing Poster because he "lost" himself. Lazarus's item, the Pandora's box, doesn't make sense because Lazarus was one of the people whose life was touched by Jesus. Lazarus was essentially pure, of course his item would be pure evil and because of that, his item doesn't make sense. None of Eden's items make sense because Eden isn't human. The items don't make sense because they wouldn't be recognizable. And to top it all off, The Lost's items for beating Satan, The Lamb, and ??? are all things that The Lost has lost. His mind, his body, and his soul.
Looking closely at Larry Jr. reveals that it's constantly crying. And why not? Its parents were killed back in Super Meat Boy.
Why does having flight allow you into a Curse Room without taking damage, but still hurts you on the way out? It's because the spikes are facing into the room, meaning that Isaac must prick himself trying to squeeze his way back out!
"Locked" characters are tied up, so when Isaac "Unlocks" them, he saves them. He saves a sibling and wishes them luck before trying to survive!
Lust's only attack is chasing after you, why not? Lustful people tend to chase others.
Rebirth adds a secret character, The Lost. The only way to unlock this character is to die repeatedly. In other words, lose the game.
And why can't this character gain any hearts? He's a ghost, so the food health upgrades just pass through him. He's already a soul, so soul hearts are ineffective, and since he's a holy ghost, dark hearts are rejected by him.
There are 31^8 possible seed combinations (excluding 5, I, O, U, and V). This turns out to be a Bible passage — Deuteronomy 31:8. What does the passage read? "The Lord himself goes before you and will be with you; he will never leave you nor forsake you. Do not be afraid; do not be discouraged.”
Why does the Lamb, a reference to Jesus, look demonic and get fought in a place lower than Hell itself? Well, it has been suggested that all of this game is essentially happening in Isaac's head, so the bosses appear as Isaac would view them. Isaac's probably too young to know much about the Bible or Christianity, but he knows that "God" is supposedly ordering his mother to kill him. Thus, it's not unthinkable that Isaac would view the Christian God (and by extension, Jesus) as a greater evil than Satan, hence the Lamb's appearance and position in the game.
Why does the Bible beat Mom instantly? Besides the story reason, I mean. Well, she's obviously deranged and could be considered a Christian In-Name-Only, considering she only seems to follow her own bizarre interpretation of the Scripture. By showing her the Bible, you're revealing to her how off base she really is and she's unable to handle having her worldview shattered.
Rebirth added a character named Azazel, a demon that starts with flight and a short-range laser attack. He's considered to be the most powerful character in the game. However, he's so powerful that winning a game as him isn't as much fun, which takes away some of the game's soul. That's right — when you play as Azazel, you are selling your soul for power.
Even the way you unlock him ties into this: you have to make three deals with The Devil in the same run, which involves trading your maximum life away for powerful items.
And even that ties in to making the game less fun. It's well known that devil deals are the easy way to victory, and thus even they take away some fun because of their reliability.
Many of the Keeper's unlocks either benefit only himself or are just straight-up not very good. Then again, he is pretty much a playable Greed, and given Greed's tendency to be, well, a greedy jerk...
The final ending explains a lot about the story. It's shown earlier that Isaac's Mom has put up posters for her missing child, and she eventually finds his bones in the chest he's suffocated himself in. Now, Isaac's remains have clearly been there a long time, given they've decomposed already... why did it take her so long to simply look in the chest? The final ending explains this and Isaac's method of suicide: the chest used to contain their family pictures, with Dad burnt out of all of them. Of course a chest stuffed to the brim with terrible memories would be the last place Mom would look!
Why is Delirium immune to the Chaos Card? Because it already represents chaos itself, mainly Isaac's mind breaking down.
Mulligans will occasionally spawn in a room with fires in it, and almost inevitably they'll end up killing themselves by walking into it. They're too stupid to notice it's there, right? Then you remember that they're people who are being horrifically mutated into hives for insects, and it's clear from their sobs that they don't like it, and you realize that they're probably trying to commit suicide.
Same happens when they're left alone for a while, they'll just decide to blow themselves up.
Which begs the question of why their bomb-carrying variants want to blow you up too. Unless they're so depressed for their existence that they're taking you with them.
You'll notice that the bomb is jammed into their head. Perhaps that bomb has taken over their brain and wants to kill you?
Although, as it is likely that the Mulligans, along with all the other enemies, are actually Isaac, then killing him would be the only way to truly commit suicide and end their existence... The non-bomb varieties tend to run away from Isaac as well — like they don't like him much like themselves.
The corpse that's in both the shop and hidden rooms has an uncanny resemblance to Greed. At first, seemingly a coincidence. Then the fact that Greed only attacks in these rooms implies that for whatever reason, Greed is playing dead on the occasions he doesn't attack...
Also Fridge Brilliance because his name is Greed, and when he sells you things, he...you know...takes your money.
Which also explains why he has a higher chance of spawning when you've visited a shop before or have a large amount of money; he's trying to take more money from you than you could pay him by buying out his wares.
Just to drive the point home. In Rebirth, bombing the shopkeeper has a chance of dropping the Steam Sale, Greed's drop item. Also, having Infestation 2, which spawns friendly spiders when you kill something, will spawn a spider when blowing up a motionless shopkeeper.
Which makes it all the more satisfying to blow up the shopkeepers to get back at Greed for all those times he screwed you over.
There is a between-floor nightmare where Isaac is suffocating in a chest. Beating It Lives for the first time gives you an ending where you find ??? in the chest. ??? is dead. There are a few endings that imply that Isaac went into the chest. Do the math.
The Ankh item resurrects Issac as ??? if he dies. One ending has him dragged into the chest by Mom. You work it out.
To anyone who gives Isaac cancer (a trinket, boosts tear rate) and decides not to swap it out when another trinket spawns: You gave a child cancer and neglected to cure it. You monster! This is all the more tempting, given how useful a more tearful Issac is.
And in a cruel irony, the trinket's description in Rebirth is "Yay, Cancer!", reflecting upon how useful it is.
Similarly, The Curved Horn is a representation of Isaac being demonic or demon possessed. Keeping it over other trinkets means you want a demonic (possessed) child! You monster! Again, a very good item, as it increases your damage output considerably.
If it makes you feel better, it's pretty easy to see it as Isaac carrying around a tumor.
The fact that you could literally throw the Cancer or Curved Horn on the floor at any time may confirm the above. Seeing as how the only trinket you can't drop is the Tick, this makes even more sense.
The SMB Super Fan item basically turns you into Meat Boy. Meat Boy has no skin. The aforementioned item's icon is a circular saw blade. Thinkabout it.
In the final level, the Chest, you can't bomb your way out of rooms. Isaac couldn't escape the chest, no matter how hard he tried.
Items and their effects tend to get this way if you think about them. For instance, the "Wooden Spoon" or "Belt" items makes Isaac faster... because he's running from being spanked! "Squeezy" may have been one of Isaac's favorite toys, so it makes him cry more as he holds it and remembers the good times in life (which is why he also gets two soul hearts). This also means when you get a pill that decreases tear damage/speed/range, you've actually made Isaac take something that makes him feel better, so he's crying less... even though this is portrayed as a negative thing.
Think about it. A Tears Down pill is actually an antidepressant, so Isaac cries less; conversely, Tears Up is a depressant! What the Hell, Player??
Then again, making Isaac cry more means that he's more likely to survive. It's sort of like how making someone aware of how much shit they're going through would make them more able to deal with it in the long run.
On a similar note, Bad Trip is normally just some drug that hurts Isaac. But when he's at 1/2 heart, it becomes Full Health. Isaac's so hurt that giving him the Bad Trip drug makes him hallucinate and become more pain resistant, allowing him to keep limping along.
There is a "Max's Head" item that makes Isaac's tears bigger and more powerful... There's also a "Lunch" item that is a dog bowl with the name "Max" on it... no wonder Isaac's tears get stronger because of "Max's Head"... it was his pet dog!
Ipecacis a serum that makes you vomit. It was used to expel poison from the body; however, ipecac itself is poisonous and has many of the same side effects. Moreover, it has been out of use for nearly a century and it is in fact recommended to throw it away. Why would Isaac's mom still have this?
The familiars have names like Sister Maggie, Brother Bobby, and the like. Either Mom had multiple miscarriages/abortions, or this isn't the first time "God" demanded a sacrifice...
Many of the "Humanoid" monsters look like Isaac. Why are there so many of them? Unless "God" demands many a sacrifice....
The Disc One final floor is the Womb, which is basically Isaac's mom's womb. It's not as bad as it sounds, until you realize what sorts of things Isaac's mother actually has in her womb, possibly including a tapeworm, a fallen angel, or the physical representation of death, depending on the RNG's benevolence.
Not only that, but her womb is actually divided into rooms.
One of these rooms can be a library. Isaac's mom literally has a library inside her vagina.
There's also a boss there called Teratoma. Teratomas are tumors with human body structures such as eyes, arms, legs, and teeth, and are generally present from birth and can be passed on from mother to child. Let us remind you that you fight the Teratoma in The Womb.
Take a look at the remains from a destroyed pile of poop. It looks remarkably like a smiley face. Is Isaac playing with the poop and making faces?
Afterbirth gives us the Burning Basement. While the environment combined with the music is pretty awesome in itself, it does make you wonder — why is the basement on fire in the first place? Is Isaac's mom that determined to sacrifice Isaac that she is willing to burn the whole house to the ground just to take him down?
There's numerous flies and poop piles in Isaac's basement, the flies are enemies, and the poop is rewardable vandalism material. Wearing an item called skatole, which is poop, deters flies. Yet you can't just grab a poop pile and smear it over yourself.
Maybe the Skatole is a notably solid poop that Isaac can carry around.
What kind of shopkeeper locks the store so that customers can't come in unless they have a key? Talk about being bad for business...
Greed doesn't want ordinary customers. He wants customers so desperate that they will hunt down keys to get to him. You might as well ask why Greed sometimes tries to kill them.
Fridge Brilliance: if you expended a key to enter the shop, you would be more likely to buy something after entering, even if this thing is another key to replace the one you used. You wouldn't want the key to have gone to waste, after all.
On the other side of the coin, the shopkeeper could have decided to close down for good and locked the place up so folks would know there's nothing to buy. Isaac loses coins from buying things because he's too kind to just take them. Greed just randomly lurks in shops and secret rooms to steal Isaac's money.
The Forsaken. Why is there a posthumous version of a ghost?
Or maybe he's not the posthumous version of the Haunt so much as the "didn't bother to get dressed" version.