These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: To the Moon
Esoteric Happy Ending: Johnny fulfills his wish; But... because they're only changing memories, not the past, the real Johnny dies never knowing what his wife was trying to tell him, and the real River dies knowing Johnny never understood/remembered what she kept trying to hint at. Well, assuming any of it was ever real to begin with.
Why didn't River just tell John about their first meeting, without going through the whole rabbit ordeal? At first it seems that it's only due to her Asperger's, but revisiting the first part of the story, it becomes apparent that she wanted, in her own way, to bridge the gap between them by reminding him of (arguably) the only time when they truly connected, and that wouldn't work unless he remembered on his own. When you realize that River made the rabbits to try and remind Johnny of their first meeting. And that when the white rabbits didn't work, she tried a yellow one, because the moon is yellow. And that when the yellow one didn't work, she managed to make one with a yellow belly (for the moon) and blue head and feet (for the sky and stars). To add an extra layer to it... Her wedding dress was yellow and blue.
Fridge Horror: During The Stinger, it's implied that Neil might be dying. And once you think about it, you come to understand why he's constantly acting immature, doing stupid things, being mean, jerkish and funny: He's trying to make the most out of life before he dies...
It's implied that all of the game's events in fact take place in Neil's head, quite possibly while he is in a similar state to John. Consider the Deja Vu of the squirrels running along the same path twice, almost like a glitch in the matrix.
The first theory is further hinted at the very beginning of the game, in an optional scene you could miss entirely if you played as Eva: the mock RPG fight against the squirrel. If you check Neil's health bar, you'll see it's not full. If you play with Eva, the bar will be full.
To support the theory that Neil is dying, at the carnival when they meet the fortune-teller, Neil refuses to see his future, saying "Good or bad, I'd be screwed either way."
Another one which makes you realize how truly screwed Johnny is: The reason Johnny's mother made him take the beta blockers which made him forget about his dead twin brother was because his mother was Driven to Madness by Joey's death and wanted Johnny to become his Replacement Goldfish, which puts her straight into the Abusive Parents field.
The agency is called Sigmund Corp. As in Sigmund Freud, the famous psychologist.
Izzy describes Johnny as "neurotypical," which is not a word that's thrown around much outside of people who know a few things about the ASD spectrum
Tony Attwood is mentioned. If you already know who he is, then you know what's going on with River.
Part of the code in the background when you prepare a memento says, "Step twice into the river of life." If you're familiar with philosophy, this is based on a quote from Heraclitus, a Greek philosopher who said, "No man ever steps in the same river twice."
Glurge: Even if the story aims to be an uplifting tale, there are still the issues of the real pain and suffering undergone by the real people, and the fact that the happy ending was experienced by only three people.
Harsher in Hindsight: When you discover that Johnny's mother wasn't just calling him "Joey" as a cute nickname, it frames the entire first half of the game in a different light. Johnny's seemingly-pathological desire to stand out and be different suddenly makes a lot more sense when you realise his own mother favoured Joey so much, she forced Johnny to become a copy of him - right down to Joey's love of Animorphs and Pickled Olives - after Joey's death.