This game is a ton of fun, and I cant wait until the next patch in a few days.
That being said, i have some theories as to who the murderer is. If you have not done all of the scenarios as far as you can take them, some of this may come as a spoiler.
Note: I am assuming for simplicity that the killer is the same in all scenarios.
Prime suspect - Jack
You may all recall the white thing in the woods. Though we may not know exactly who/what it is then...it was most likely Jack. We know he has been in the woods for about week, and he is a shady character. He pulls a knife on Dave and chases him all the way to the mansion. While he has not been visible in story that long...his unknown part in the story makes him a prime suspect. The knife he pulled could have been the one used to kill Hoss and Oswin, or have been in the Floor with Sal, and could have been used to slash up Tyson. We also know there was an unknown figure in the mansion on the night Roswell dies.
One of the big incriminating clues that this will be the murderer is Oswin's Hansel and Gretel story.
Second suspect - Orlando
I know this is going to surprise a lot of people, but Orlando could be the killer in every scenario (even his own demise). Looking at Orlando's backstory, his family is in the mafia, and his family is looking to have him take over the family business after the vacation is over. Usually in the mob, there is some sort of "test" when handing this type of thing over. His test could be to kill one (or all) of his friends.
When you talk with Thantanos in the lab, he talks about how they obtained DNA of Orlando's dad, which also means Orlando could be programmed into the Vault.
A lot of the bad endings and the investigations that come in the good endings hint that almost everyone would let their guard down around Orlando because he is trustworthy.
On top of that, he can be tied to every one of the killings:
Tyson - claw marks mauled the body. Sal also watched the incident between Tyson and Dave leading up to Tyson storming off. If Orlando found out from Sal, that gives more than enough motive.
Sal - He knew early on about Sal's sleepwalking (which is evident in the Sal story). Orlando also knows the freezer sticks, has access to the knife that was in the floor. The reason it still makes sense here is you pass Sal off to Orlando ONLY. If Sal were to be found dead, the only suspect would be Orlando, so he backs out.
Hoss - after Tyson thinks he kills Hoss, and Dave heads down to check, Orlando is on the way to the gym. Orlando also has the most access to the knives.
Roswell - while there are no direct clues here, Roswell says he'd be safest around Orlando and would willingly turn his back to him.
Dean - This one is the biggest clue for me. Before Dean dies, he goes to feed Dave a mushroom and Orlando swats it out of his hand. Dean then picks the mushroom off of the floor and eats it which leads to his death.
Orlando's ending - this one is a bit of a stretch...but here it goes. Say Orlando was tasked to kill Dave and friends. When Dave tries to buddy up with Orlando, Orlando decides it is not worth it to follow through and commits suicide. He is also smiling which would indicate he was happy with his decision. One of the other awkward parts to this is in the bad ending, the vault is OPEN!
Oswin & Benson - There is no real evidence for or against any of the characters with regards to either of their bad endings.
Third suspect - Oswin (aka OZ)
The reason Oswin is one of my top suspects is because when you read the letters, some of them seem to apologize and he did not mean for these things to happen. My guess that the first couple of deaths were "experiments" to test Morphic Resonance. He also knows about all of the secret passageways and secret rooms, has the chemicals used to kill Dean and Orlando in his lab, and has the house bugged. Benson also hints that we should not be too quick to trust Oswin. He also has access to a gun (he fires at Jack), and has the air gun thing to inject chemicals into people (which would have been used to kill Orlando).
Potential other suspects: Dean and Roswell.
The argument I have seen for Dean (and could believe) is that he is the jealous boyfriend, and kills whoever swoops in on you. Dean's death could be chalked up to an accident. One interesting side note for Dean, is that in no scenarios except his own does he help in the investigation.
Roswell has a similar side as Dean, except instead of boyfriend, he wants Dave as his absolute best friend. He talks about wanting things to be the way they used to be (when he was Dave's only friend). He also seems to be incredibly knowledgeable about just about any scenario. He knows the chemical to kill Orlando, about dangerous mushrooms that kill Dean, and about Hypnos (who controls Sal while sleepwalking). He also was near the room when Hoss was found stabbed. He also seems to know about Oswin before he comes out (it cannot be coincidence they are both boars). I believe there is also a reference that Florencia might be Roswell's mother.