In the Shower room where you find Snake's supposed body, Santa talks about how the human body dies at 75 degrees Centigrade after examining the thermostat. He says a human body could only get that hot if it was in a sauna too long or.... in an incinerator...
When Santa finds the perfect Panty Shot angle in room 6, why does he tell Junpei to go get Clover, when June is actually in the room with them? Turns out June is his sister, and the two of them orchestrated the whole game.
The "Previews" from the main menu. Why give the option to rewatch what is essentially a game trailer? They show you which doors need to be taken in order to unlock the True Ending.
Subverted with one showing a shot of Lotus at the computer with dark eyes, as it may be hinting the doors not to go through (4 and 8) or she'll get angry at a remark, so you can't get the Safe Ending.
Similarly, take a closer look at the 'Memories of Escape' option. They're listed in this order: the room you begin at, the four sections that lead to the True Ending, the three sections for the Safe ending, and then the remaining rooms (which lead to the Sub ending, the only other one with credits).
In the knife ending, Junpei himself is unable to recognize his killer due to being practically dead from blood loss, despite seeing him leave. It turns out that it is a hint about his killer. Ace has prosopagnosia.
In Door 6, Ace estimates about four engines of this size would power the ship. Ace has been on the Gigantic before (and its owner,) and recognizes the surroundings, He would naturally know the design.
In the Second-Class Cabin, on the subject of the Titanic, June believes Stead telepathically saw images of his own future, namely his experience on the Titanic. A less subtle hint about Akane's own state (though she saw it through Junpei's eyes.)
The very last puzzle has the player turn the DS upside-down, reflecting that you're now playing as Junpei instead of Akane, which you've been doing up until that point.
Throughout the game, Akane continues to insist that they can find a way to end the game with everyone alive, which seems to serve to highlight her naive and optimistic nature. At the end of the True Ending, we find out that she knows how the game works, and that it's designed for everyone to escape alive.
If you go through the True Ending, you find out that the "9" door that you need is actually a "q". There's one other door with a Q in it though - the Captain's quarters! You need to go through there to reach the True Ending and find out about the true nature of the Nonary Game from Clover.
What do the correct door paths to the True and Safe ending have in common? They're the only two possible paths that let Junpei partner up with every other participant at least once. Select any wrong door, and you'll miss out on working with one or more persons.
Door 9, well, the various doors numbered 9, are behind door 6, which is both the number 9 upside down and Akane's number.
During the doll-presentation flashback in the True ending, Junpei says to Akane that now that they're graduating from elementary school, "after June we won't see each other anymore". Word of God says that after the Second Nonary Game in which he gave her the alias "June", he never sees Akane again. (This is a brilliant Woolseyism; her original Japanese alias was "Murasaki" and had nothing to do with months.)
In the 'Safe' ending, Junpei learns from Santa Ace's real identity, and that Ace told him this himself. Given Ace already killed two people to hide that fact, why would he tell Santa? Easy; he didn't. Santa is one of the masterminds behind the game and knows exactly who Ace is.
The 1st Class Cabin gives us this little hint to Snake's name, Light, on examining a lamp:
Junpei: Well, at least we've got light.
Snake, surprised: ...
The "Submarine" ending hints on Junpei, Seven, Lotus etc's killer. Lotus' wrist is missing a bracelet, Seven and the rest aren't (though Ace's is unseen,) and the remaining door is a 9. The only other known bracelets are the 2, and the 9. Do some number-crunching, and you will realise 1+8+9=18 is the only number that fits.
Some other endings hint at this, too. The disappearance of Lotus' bracelet is also remarked on in the "Knife" ending, and in the "Ax" ending, Ace wants to show Lotus something special while Junpei remained at the elevator to wait for Clover and the others.
In the True Ending you find out that the last "9" door is actually a "q." This works better in the Japanese version because the Japanese word for 9 is "kyu" and is pronounced like the English letter.
This can be considered written around in the English version, when you realize that Zero never verbally says the last door is a '9': just the typed rules given to everyone where the font makes '9' and 'q' look the same.
The digital root of the doors you go in determines the number of the person who gets the gun in the two endings where the gun goes into play. Safe ending is 586. 5+8+6=19, 1+9=10, digital root= 1. In the Safe ending, Ace gets the gun. True ending is 471. 4+7+1= 12, 1+2= 3. In the True ending, Santa gets the gun (at first).
Speaking of which, about that... The gun is hidden in such a way that someone must put the correct cards with faces of the various characters on them into the correctly numbered cases to get it. Ace has no means of getting the gun without someone else's help.
Should you choose to go back to the hospital room while searching for Snake, Santa will tell Junpei that he shouldn't trust anyone in the game, not even the person he's closest to. Being one of the masterminds behind the game, he knows exactly who can be trusted and who can't—the latter group including said person Junpei is closest to.
Through the various endings, Junpei frequently has a Heroic BSOD where he becomes a 'shell of his former self' and is 'no longer Junpei.' In most circumstances, this is the result of June's death. Watching the events from the past, Akane's horror at learning of her own death is entangling with Junpei's, making it hard to tell who Junpei any longer. The only time that Junpei recovers from these shocks quickly is when he confirms that she had died in the past; a shock, but a paradox that the both of them can push aside their despair for to try and puzzle through it.
Also, when in the Captain's Quarters there is a spot where you can have a major plot conversation with Clover, but if you didn't satisfy the conditions for the conversation Junpei will remark about a sharp pain in his chest. Missing this part of the conversation leads to the ax ending where Junpei is hit with an ax. I interpreted the blow striking him in the chest as it didn't instantly kill him.
Actually, it's implied that she chopped off his hand to get his bracelet off. This is the reason why she offers her hand to Junpei, rather than just striking him down in the first place; she wanted to sever his hand cleanly. This also explains how Junpei is able to see Clover walk away with his bracelet when it's not supposed to fall of until after it detects his death.
There are actually three doors with the number 9 (at least, originally, before Zero changed the last number 9 door to a q.) Remember the title of the game? 999.
The key to the final room in the "good ending" has the Neptune symbol. The astrological sign associated with Neptune is Pisces, and the symbol of Pisces is two symbiotic fish swimming in different directions. Seems like some subtle foreshadowing of the ultimate significance of the Junpei/Akane relationship
Santa mentions his success on the stock market which first makes him look like an intended victim for investing in the corrupt corporate empire, but Word of God reveals this was actually the source of Zero's funds and enabled by her visions of the future.
June's fevers and Seven's headaches indicate you are on an incorrect path, causing young Akane to burn and discrepancies with Seven's false memories.
Everyone remembers Akane as dead, even in the true ending when she never died. Why? She planted the thought in their heads. The Morphotrogenic field is used both to implant ideas in the heads of others as well as to receive ideas yourself, remember, and Akane is clearly very, very good at accessing the field, and is a stronger 'transmitter' than 'receiver.' She also knew, upon existing the incinerator, that she needed to have died in order to survive, and so she overrides everyone's memories of the event with the event that never happened, that of her being burned alive, resulting in false memories for all involved. This might also explain why June doesn't seem to know much more than anyone else about what the true path is - when young!Akane changed the perception of the events in the field she changed her own perception of events as well, which left her hazy on the details of what decisions led to what end.
The joint digital root in alphanumeric of "I am Zero" is ... Almost certainly unintentional, but still cool.
Another hint about the connection between June and Santa: when everybody is showing their bracelets, only they have sleeves covering theirs, which might also indicate that they're immune to the bracelets' constraints (being 0 and 9).
June's bracelet looks like a 6, but is really a 9. Going with the Enneagram motif, June herself looks like a naive peacemaker (9), but is really a mistrustful, cunning genius (6).
It should have been obvious from the start that the nine players aren't on an actual sinking ship: both times when Junpei checks the flooded stairways, the water is described as being completely still, like a mirror. The water shouldn't be still - the ship would be, at the very least, bobbing on the waves!
Why did June pressure Junpei so much on details about his kidnapping? Because she never saw it happen, and she has to perform it herself. She's relaying all the information to her past self for later past use!
Why does The zero bracelet read as ? If you choose to not believe that it's "o", then it's simple: It's a hint that Akane (who has designated herself as "6", is in fact Zero.
And if it is an "o", then in any base higher than 24, the letter o represents 24. The digital root of 24 is 6, and adding 24 to any number affects the digital root the same way adding 6 would.
Snake shows in the Safe Ending that he has the willpower of a god. This is not anything recent, though: in the flashback of the first Nonary Game, he tells the other kids (as a little kid himself) what he got his sister, Clover, for her ninth birthday. Nine four-leaf clovers. Finding even one four-leaf clover is rare enough that it's considered a sign of good luck. Snake went out into the fields and picked up nine for his sister's birthday present. And let us not forget, Snake is blind. He did all this without seeing. His willpower is over 9000!
The digital root of each set of numbered doors you encounter adds up to 9.
First set: 4 + 5 = 9
Second set: 3 + 7 + 8 = 18, 1 + 8 = 9
Third set: 1 + 2 + 6 = 9
Final set: 9 + 9 = 18, 1 + 8 = 9
This is really just a necessary side effect of making it such that each set can be explored in parallel using all participants.
According to the Enneagram, each type will resemble a specific respective other when under stress or when at its strongest. Snake is a 5, which "disintegrates" with 7; Santa is a 7, which integrates with 5. The player sees Snake losing his composure and Santa at the top of his game with a common catalyst.
Junpei gives odd descriptions of corpses such as comparing them to a macabre crab with pizza dough spilling out. Those descriptions are actually being made by a 12 year old Akane, how else would a 12 year old describe a corpse with such limited vocabulary?
Akane's behavior throughout the game, teasing Junpei, but also acting oddly innocent and seemingly not always realizing when she's doing something to turn him on. All in all, you could say she's acting more like a 12-year-old with a crush than a mature 21-year-old, couldn't you? She knew that her younger self was watching her and didn't want to do anything that the younger Akane wouldn't do, so she basically acted like a 12-year-old all game long. And, yes, from what little we can see from flashbacks, Kanny did tease Jumpy quite a bit when they were younger, though her teasing was obviously a tad more innocent in nature.
The Safe Ending finishes with the time limit being hit and Zero being announced as the loser, after telling Junpei that he took the wrong route. Going through the True Ending, we find out that Zero is Akane and that she is using Junpei as her "transmitter", using the morphegenic fields to see what he's seeing and escape the game. As we also find out, the reason she does this is because she winds up trapped in the incinerator and needs Junpei's help to solve the last puzzle and survive. Because Junpei took the last route, he didn't make it to the last puzzle on time. Thus, he was not able to help Akane solve it. Thus, Akane either drowned or burned to death.
Thankfully due to the nature of the Timey-Wimey Ball that future never happened and in fact it was a part of her plans.
And no one else thought it was creepy that Akane's fevers were because you weren't doing it right and she was burning to death in the incinerator?
Furthermore, She may have suffered it several times, depending on your interpretation. It's a wonder she kept so much of her sanity...
On a similar note, Junpei's "misunderstanding" conversation with June at the elevator is hilarious... until you realize it's pretty unlikely that June's description of drowning would've been "heard from people who have experienced it", as she claims. Instead, in this context she's probably describing her own experience of drowning in an alternate timeline.
It's not so far-fetched that she has met or read about someone who was narrowly saved from drowning. But considering she describes the fuzzy, free-floating feeling right after saying "I'll go to Heaven," there might be something to this.
Chances that Akane actually drowned are pretty much zero. Considering her fevers mean that young Akane is being burned in the incinerator, and the present game actually takes place in Building Q, she would have never had the opportunity to drown - unless, of course, you count her feeling it from Junpei's experience in the Sub ending.
In the sequel, whenever the main character dies, he describes the free-floating in a void feeling each time. So we can pretty much conclude that this was what Akane was describing. If that is the case, then she is describing a very general after death experience that she could have experienced many times.
The scariest thing about the sub ending isn't that almost everyone died. It's the fact that Snake is still trapped in the coffin and has to starve to death or run out of air while not knowing where he is and being trapped in a small space.
Totally what I thought too. The same thing probably happens to him in the knife and axe ending because no one took the note.
Unless Clover takes an axe to the coffin when she hears someone in there.
Even worse, if she chopped the coffin open and found out Snake was still alive, not only did she kill everyone for no reason, but the two of them can't even escape because the final exit door is actually a q.
Just imagine what would happen if this DID happen. If she doesn't kill him before knowing who he is, she'll certainly, dare I say it, become even MORE of a maniac. I mean, she killed everyone out of revenge for him, and then killed him in what could kind of be considered an accident. Most likely, this would end in suicide. And if she doesn't kill him, and merely hacks the coffin open to see her very much alive brother, what then? I can't even imagine her reaction. And then Snake's reaction to finding out she killed everyone!!! Who knows how that one would end! Thankfully, it never happened.
In the axe ending Young Akane says thatClover is surrounded by light. Where is this light coming from? The fire from the incinerator that she's trapped in.
Think about the cryptic line from the Safe Ending ("You haven't lost... I have lost."). Now think about who is probably saying it. Ouch, Aoi...
In the axe ending, Ace and Lotus go off to investigate a corridor shortly before Clover shows up and kills Junpei. Now, think about why Ace would want to have Lotus alone. He has his  Bracelet and the  Bracelet. Chances are extremely high that he wanted to get Lotus alone, and kill her to take her  Bracelet, with which he can escape by himself, or so he would think until he hits the q door and dies.
More like Fridge Squick, but from what I can gather, 12-year-old Akane is tapping into Junpei's mind throughout the game and can see and hear everything Junpei sees, including his inner monologues. With that in mind, look at this exchange again:
Akane: Hey Jumpy, do you want to take a shower together?
Akane: *giggle* Just kidding.
Junpei: Too late to take it back... My brain's already working out the picture.