My first suspicion was Thomas because he was very particular about his Squirrels, and there were red trees dotted around the town so I decided to find out where they all were, one of them was at the Police Station.
My second suspicion, in the 1st chapter I think, was George because I followed another red tree to his house! At this point I realised that he was in the forest looking for you when you first encounter the RK. But I can't remember if he can be accounted for the other times. I seem to remember him and Emily just stand outside while you're inside tripping or whatever, so did George just wander off and leave Emily alone? I dunno, I need to play it again.
It was also hinted when he pushed that massive tree statue, which should be impossible, so he obviously had some superhuman strength. And the subsequent deaths all happened when he was there, I think? He made the tree unstable for Diane, and cut the wire for Becky (?). The clues are definitely there, and there's so many red herrings, one in particular being York himself, that it's hard to pick out what's relevant.
I never suspected Keysen, because I felt it was so utterly ridiculous that he was involved in anyway, or perhaps it was too obvious for the travelling seed salesman to be the bad guy. Either way, I think it's incredible how the clues really were there for you to pick up on, but instinct tells us to ignore it, and that maybe York read his coffee wrong. The picture behind Polly was just the icing on the cake though, I mean, how ballsy is that: putting the answer to the entire mystery in front of your face every time you wake up.
In the end, all 3 were involved, but because the game focusses so much on the RK being a singular threat, it deters you from the very idea that more than one person could be involved.
Also, wasn't there another Brian referred to in the story? Aside from the gravekeeper that is? Could they be the same person.