I actually just downloaded the developer commentary but haven't watched the whole thing yet, so that may change my opinion depending on how in depth Matt goes as to the meanings behind the game, but right now this is just my personal interpretation. I also subscribe to the "death of the artist" idea where art can mean something different to the person experiencing it no matter the intent of the artist, so I'll totally hide behind that if I'm ridiculously way off

I'll kick it off with my favorite ending: Wayward Dreamer. After being chased through the house by murderous dolls, which I took as one of the many different manifestations of his need to be punished for what he feels he's done, in the last scene, Thomas walks into his sister's (finally normal looking) bedroom to see her sleeping peacefully. He leans over, gives her a kiss, then walks away as it fades to credits.
I loved this scene for its poignancy and closure. I took it as Thomas finally making peace with his sister's death and letting her go. My overall story theory for this branch, which is the first one I played once the final game was out, is that Gabby died to an accident or maybe illness when she was six (date on the headstone), and Thomas has been struggling with the guilt and depression ever since, blaming himself for not being able to prevent her death. Even if he couldn't have done anything about it, he feels responsible somehow, as shown in the scene where he's running after her in the forest but just can't keep up. Now, how she died isn't clear, but it's also not important, I don't think. The key thing is she died at six and he feels responsible. Knives are a common thing, but my take is that's just another manifestation of his depression and guilt. His nightmares torment him in the form of him taking her life by his own hands, but that's just a depressed and guilty mind twisting his nightmares. There is a lot of symbolism involving disemboweling, so I'm probably missing something else there too, but that's my interpretation of that particular branch.