This discussion may contain spoilers!
Since we are possibly very close to finding the real murder of Fabletown, let's go through all of the characters and see who is most likely to be the killer and boss of the Crooked Man.
Bigby - Believe me, at first I thought Bigby could have been the killer because of some weird magic that controlled him but that seems rather stupid so Bigby is off my list of suspects for now. But the reason I thought it was him was because of the Huff n'Puffs that the killer smoked, just like Bigby, and the fact that all of the kills have an association with him (Lily was glamoured as Snow and Faith was helped by Bigby).
Snow White - I am quite suspicious of Snow ever since she has been doing other kinds of business that we have no information of. She did not seem shocked by Lily's death and the fact that she was glamoured as her, she didn't seem very saddened by Bigby's broken arm and she also doesn't seem to care about the price of the glamours even after seeing that a lot of people buy black market glamours instead. But she is in the comic books alive so therefore she might not be the killer, but that doesn't make her an innocent since she may be the one behind this by accident and maybe the plot for a possible season two would be to save Snow from her evil self.
Toad, TJ & Colin - I put these three in some sort of group because they are the main Farm characters as of right now but also because they really don't seem like the killer to me. After all, they're animals! And they have never shown signs of being the killers.
The Tweedles - Honestly, who would work for the Tweedles? They seem quite unpowerful and dumb. They are involved though because of course they are the ones who make the dirty work of dealing with Bigby and saving Crane's ass.
The Woodsman - Quite unlikely since he looks too sensible and good to do such a thing. He also shows a lot of support towards Bigby in episode 4, but he seems to know who it is since he does contradict the Jersey Devil when he says that there is nothing that Bigby can do to save Fabletown.
Nerissa - Like all the other prostitutes, Nerissa seems to be the puppet behind all of this, which is why she's off my list too.
Bloody Mary - Mary seems to be the on cutting the heads since she must find a lot of joy with that. But she seems to be quite loyal to the Crooked Man, her boss. So she may be the physical killer but she is not the one who orders to kill.
The Crooked Man - I honestly don't think it's the Crooked Man at all. He wants power and money so what would he get with killing his clients? There must be a secret that the prostitues can't tell which is why they can not take off their ribbons and it must be something extremely important.
Georgie Porgie - Georgie seems to be the one who is just doing his job of looking out for the prostitues, again he is not above the Crooked Man and doesn't seem to have the guts to kill anyone.
Vivian - A lot of people seem to think it is Vivian but I highly doubt it. She is just the leader of the prostitues and wears the ribbon too, which means that she is also controlled by the Crooked Man.
Ichabod Crane - Crane just doesn't look like he has the guts to kill anyone either, much like Georgie. He also seems to be quite frustrated with the Crooked Man when he tries to incriminate Crane. Off my list.
Jersey Devil - Jersey is very loyal to the Crooked man (even though not as powerful as Bloody Mary) but he doesn't have a lot of reasons to kill.
Beauty & Beast - If one is involved, the other one is too. Beauty & the Beast seem to know more than what we think. Although they look like just the couple who is too shallow and therefore has to live in debt for the Crooked Man.
Bufkin, Johann & Dr. Swineheart - These characters are very unlikely since they appear in the comics as good people. They all seem quite powerless for such a crime. (see Faith & Lily to know more about what I think of Dr. Swiney)
Bluebeard & the Headless Horseman - I grouped these two because they both have a history of cutting heads. Bluebeard is only interested in money and according to the comics, wants to leave his past behind also. The Headless Horseman has been just briefly seen at Crane's apartment in the form of a statue but still, why would Crane keep such a thing?
Faith & Lily - Again, quite a few people think it was Faith who caused these accidents, or that maybe it wasn't really her who died and that it was someone glamoured as her. I kind of agree with that theory 50% since glamours fade away but maybe Dr. Swineheart who is in charge of the bodies is hiding their true identity to Snow & Bigby.
Lily, Gren & Jack - Although they don't like anyone from the Homelands they would never kill anyone from their 'homeland'.
Lawrence, Magic Mirror, Clever Hans, Aunt Greenleaf, Tiny Tim and Cryer - All of these guys seem to have little to know screentime in our games which makes me think that neither is behind the murders. Lawrence has a determinant state which takes him off of the list, the Magic Mirror is just a mirror and doesn't have any control, Clever Hans seems too powerless to do such a thing, Aunt Greenleaf is just in debt with the Crooked Man and only wants to keep making money in order to survive, Tiny Tim is just the guy who was offered a job by the Crooked man but doesn't seem like he wants any kind of trouble with it either and Cryer (who is not even a definite character yet) seems to be just a model for Telltale.
'Long Live the Queen' - Did anyone notice this phrase? It was said by Bloody Mary after breaking Bigby's arm. It's possibly a hint towards that the killer is a woman.
I know this is a pretty big post but these are all the characters (Fable wise) that have been introduced in this series of game. Let me know if I missed anyone or your opinions on the characters.