Speaking of Bonnie — I think we can safely rule her out as Wes' murderer. While she certainly has motive (like, say, Wes finding out that she murdered his girlfriend) it would be pretty disappointing to learn that Bonnie was the culprit in yet another mysterious murder. By that logic, Frank is likely out as well — it was shocking to see him drown Lila (Megan West) at the end of season 1, but would be a lot less surprising now that we know his murderous tendencies occasionally rear their ugly head.
Then there's the big question mark: Did Annalise kill Wes? I'm inclined to say no because of how much she cared for him, but that alone is enough to make her suspicious — the cast certainly would be shocked to learn that Annalise was capable of such cruelty with someone she loved.