before I start i'd like to say sorry for the bad english, 'cause it's been a while since i've been on an international forum x)
WARNING! Wall of text coming~~
Well.. this theory started with a discussion I had with a friend who is still reading AGOT... somehow the subject turned to Jon Snow's Parents and i was wondering if Varys knew about his mother or not(I go by L+R = J, that's why i though it was worth wondering)... for my surprise, she answered that he knew, when I asked why she said something like: "it's his character: he knows it all, he hears it all, if he didn't know something like that, wouldn't that be OOC?". At first I thought that was a little bit of a childish though...
Then I remembered once, in a soap opera that we used to watch, when a character got killed and people started wondering who did that... they first though it was his wife, then his daughter, his best friend and hundreds of different people... but no one thought it was the shows' villain, who turned out to be the murder at the end... And EVERYONE was shocked by that! I mean...sometimes the answer is in our faces, but we start to overthink things and forget that sometimes the most obvious choices are the right ones.
I started to think then: How long is Varys working for the crown? Wasn't he called by Aerys himself to spy? Aerys trust no one, not even his own son, wouldn't he put spies on Rhaegar too? You may hide a bastard that has already been born by a different name, but hiding a pregnant woman is a much harder task, so i don't really think it was that hard for Varys to find that out...this became clear to me when I was re-reading varys's dialogue with Illyrio, in AGOT:
"Yet Lord Stark's the one who troubles my sleep. He has the bastard, he has the book, and soon enough he'll have the truth. "
Which bastard is he talking about? Eddard Stark had found Gendry, it is true. But he hasn't sent him away yet, i don't even know if it was Ned stark who sent Gendry to the wall, could it be that we've been thinking about the wrong bastard after all?
Now it comes the tricky part: "If a so called Targarien loyalist knows that another of Rhaegar's sons is alive, wouldn't he do something about it?" My answer is that he already did.
---NON R + L= J part of the theory, (As my this theory doesn't really needs to rely on this fact, it's only complemented by it if it's true,i've separated that like this so if someone doesn't believe in it, it can read the "good" part of the theory without feeling angry =/)
Now, the next part of the theory doesn't really need the first one to be true... but i needed to show how I got to this, so i've started with that...
My point with all of this is that there is an actual possibility that Varys is the one responsible for the Bastard's Letter. Why? because he is the only one who would get an actual profit from that.
Varys has his little birds spread all around Westeros. It's no hard task to put a little children on the wall, mute or not, the same goes to winterfell, no one looks for the servants after all. Besides, his little birds can READ, they would know how ramsay talks, acts and writes. They would know what would make Jon go mad, they know how many men each of their armies have, they would know about Mance, the Red witch, and even about reek. He has the means to put together every single piece of information the letter contains and use it for his own profit.
How the letter helps him? That's not hard to figure out either: No matter what actions Jon takes after reading it, whether he sent Ramsay the people he asked for, put together an army to take winterfell or whatsoever, that letter would bring a massive damage in Stannis remaining troops that stayed on the Wall, as any action Lord Snow takes would cause a commotion that would crush the delicate balance that Jon worked so hard to build as LC.
That would end Stannis' "kingdom", as now he holds only the Nightfort and Storm's end(who will soon be taken by Varys' Aegon.
---/ end of non R + L = J part.
So... you may have been wondering: "wait? If that's your theory, why did you said all those things about Jon Snow anyway?" It's because, Varys may not have written that letter only to hurt Stannis, he might have other reasons to do it.
This part of the theory really depends on witch team you're on: if you believe Vary's speech, that he goes for team Targaryen, then, he may have also taken Jon from his post at the wall so he could put another person with the "blood of the dragon" in charge of somewhere: Winterfell. This way, Jon can't be dead: it would harm Varys' plan, and is being healed right now.
If you believe Aegon is fake, or that Varys is trying to put someone he "built" in the throne while exterminating all of the Targaryens, then, for his plans, Jon HAS to be dead, so his chances of surviving this are minimal: he had to eliminate Jon before the truth came to him, although that risk was minimal, that was a risk.But still, the main target of all of this was Stannis' army, Killing a targ would only be a bonus.
It happens that we've been worrying so much about Jon, and how this letter may have killed him that we forgot that he's involved in the Game too, this letter wasn't written to hurt Jon, It was made to attack King Stannis. Jon was just a pawn, and he was played pretty well.
What i'm trying to say is that we forgot that this particular part of the book can not be separated from the other storylines, why do we think that the letter was made by Ramsay, Alliser Thorne, Mance, or even stannis? this is not a Northern game. This is an westerosi game, why can't we consider that maybe Varys is responsible for that letter? he wouldn't be so sloppy, he wouldn't forget the North, if he has to attack the Lannisters so they fall and Aegon win the war, he wouldn't forget the north.
Why can't we think the letter was from Littlefinger either? Don't you find odd that Satin, born and raised in a BROTHEL knows how to read AND write? Couldn't he be working for LF too? He is in a sort of high position at the wall: he's the LCs steward, he may know a thing or two, he may even have read Ramsay's letter, and LF may know about reek, even better than Varys himself, and he also needs to wipe Stannis out of the way, he supposedly works for the Lannisters, who also want Jon out of the way, just like some people on the wall do. And he does hate Ned enough to want his bastard kid dead too.
We can't exclude the north from the bigger picture, of course there are conflicts between Stannis, the Boltons and Lord Snow, but it seems that we have ignored completely the "world domination" players here. I've seen a lot of topics discussing it who wrote the letter was, but i've never seen any of those names mentioned now, and I kind of undestand why: it took me a friend who is still in the first book to get me thinking of this, i guess it's because, as she's still in the firts book, she only knows the major players in this game and didn't forget what is important to consider right now...
so... that's my theory, hope it makes sense ^^