At the start of the game, you encounter a dresser that can't be opened until the house returns to normal. You are able to open it during the ending, if you remember. This is because Viola-in-Ellen's-body changed the house around with Ellen's magic, and Ellen-in-Viola's-body restores it back to its original state as she goes along. Its "normal" state is serving Ellen, not Viola.
The savepoint cat. At first, it seems a little strange for a randomly talking black cat to be your means of saving the game. Then the third ending reveals that the cat is a demon who made a contract with Ellen. When you really think about it, Ellen was able to revive (load a save) an infinite amount of times because the demon was directly lending her power throughout the whole game. The demon was just using the cat corpse as a vessel, so you were able to save even when it looked like he was dead. Both sides of the contract were fulfilled in the end - Ellen avoided death and the demon got to feast on many human souls. He appears in the true ending to most likely eat Viola after her death.
Viola's cruelty throughout the game, callously feeding her faithful frog to a snake, tearing a nice flower to pieces: she's really Ellen.
In one of the puzzles, you have to use a proper turnkey (Queen Key) to play a music box. The hint says "Play the music box with 12". The "12" refers to what number a queen in playng card is. However, it may also refer to how you got it from a clock.
In the '____' Ending, waiting 50-60 minutes at the start of the game seems random for an ending. But then you realize that Ellen has left Viola with an almost dead and slowly dying body. So waiting at the start will cause her to die at SOME point, causing the Rose gate at the front to die out as well. Doubles as fridge horror, knowing that Viola has to suffer an hour "Waiting" for Ellen to come in her house and take it back
It's well-known that you're actually playing Ellen-in-Viola's-body. While the picture in the menu looks like normal Viola most of the time, it turns into a Nightmare Face if you look at the menu while in a completely pitch black area. In this case, character is literally What You Are in the Dark.
At one point you enter the closet in the kitchen only to find it full of human skeletons and if you examine them you see that none of them have hands. CHEF!
The spell given to Ellen by the demon to swap bodies requires complete trust from the both parties involved. Therefore in the end even if Viola in Ellen's body had managed to stop Ellen it would have been impossible for her to reclaim her body since Ellen obviously would have never agreed to it.
Over the course of the game we come to realize that Ellen will do anything to achieve her own ends, be it kill an innocent frog and his children, murder her parents and a slew of children, leave her friend to die in a mangled body...What's going to happen to Viola's father if he ever does something that displeases Ellen?
If you go through the game without saving, some special things change. Specifically, the Witch's room where everything changes from "A vase of flowers" or "A drawer full of cute outfits" to "A vase of flowers, I love flowers" and "A drawer full of MY cute dresses." What is horrifying though is that she reads her bookshelf and it says "Lined with books on magic. It's not so bad being powerless FOR A WHILE." It seems like Ellen isn't done feeding her demonic cat even after being cured.
Reading "A Funny Story" gets someone to laugh. It might be Ellen, cruel as she is. Given how the true ending plays out, it might have been the inspiration for Ellen's plan from the start; Get through the house, find Viola, get her to chase Ellen, then get Viola shot by her own father.
The medicine Viola gets from the yellow flowers could be opium, further proved by the fact that the prisoner, when given the medicine, acts addicted and needs a jade pipe to use it.
This is even worse when you consider The Diary of Ellen's backstory. All the invisible residents of the house are leftovers from souls the demon ate. That prisoner was Ellen's drug-addict father, and the pipe was originally his in the first place. Ellen (as Viola) tosses it back to him in the game and the other prisoner (who we now know is her mother) leaves, and these events parallel Ellen's family situation in the past.
The third ending/Nonstandard Game Over '___'. Viola simply sits outside and waits until the house disappears, along with the flowers. Of course, this only works because she knows the witch's body will give out, and is just waiting for her to die. Just imagine what that must have been like for the real Viola...