That letter sounds too much like Ramsay to have been written by anyone but Ramsay. It may be full of lies, but Ramsay wrote it. I can't see any of the suggested suspects: Mance, Theon, Roose (?), someone on Stannis's behalf, getting the tone that right, even Theon.
There's a bajillion threads on it, but the long and short of it is, in all other examples of Ramsay letters, we've had blood-as-ink, the specific adjective "spiky" hand, and in two cases, a flayed piece of skin.
None of that is present in the pink wax letter. The "spiky hand" may not be such a big deal if Jon had not specifically noted it in the previous letter he got from Ramsay. It's extremely out of character for Ramsay to write such a goading letter from a supposed position of power and not include an ear, finger, skin, etc., some type of grisly trophy cut from Stannis's head. This points to someone other than Ramsay as author.
In my mind the following is most plausible: Bolton's capture Mance and/or spearwives while the Freys and Manderlys are gone. I agree with the prevelent theories about Stannis's trickery and Manderly's complicity. The returning Northmen tell the Boltons all the info in the letter about Stannis's defeat and hand him Lightbringer. All well and good, says Boltons, but where's Arya?
"Arya" was the lynchpin in the Bolton's claim. When she leaves, it's def-con 5 panic time in Boltonland, because it's spelled out for us in a bajillion ways that the Boltons can't command the North's loyalty w/o the Stark marriage. For the Boltons, the only thing worse than Arya's absence is if she runs to Jon Snow, as he can call B.S. on the ruse with all credibility.
Snow, therefore, has to be silenced. Roose's analysis is that Snow is a man who didn't act when his father and brothers were all betrayed and murdered, his sister married a Lannister, and his other sister married the most sadistic guy in the North. Roose's thinking goes, if Snow is informed that his ally Stannis is dead and he's alone in the North, that should subdue him. If it doesn't, tell him that we know about Mance, and if he spills the beans about Arya, we'll spill the beans about Mance, and let the North decide who they hate less. I'll write the letter as Ramsay, to put a little more fear in this weak-kneed, family tragedy ignoring bastard.
So, the letter was simply a blackmail attempt. The last desperate act of guys that are about to die horribly. No more, no less.