What should you call a prince of the blood, when his older brother is Aegon? This is the question Rhaegar and Lyanna must have faced when the birth of their child drew near. Of course that child may have been a girl so they must have discussed names for both sexes however this post isn't about what they may have named him had be been female. It is about what they had planned to name him if he was; as he is, a boy. What Lyanna herself may have already named him as decided by herself & Rhaegar prior to their deaths.
My conclusion after studying the text is that he was named Aemon.
In A Game of Thrones when Maester Aemon reveals his identity he tells Jon that he was named by his Grandfather. Who chose the name Aemon to honour his own Uncle Prince Aemon the Dragonknight , well officially his Uncle but the rumours say that perhaps Aemon was in fact Daeron II Father.
Straight away this ties the name Aemon to a man whose Father may in fact be his Uncle. Just as Jon's Father is actually his Uncle.
The circumstances between the two men are very different but right away Gorge RR Martin has woven in a historical figure through whom he has introduced the idea of a Father who is really an Uncle.
"Jon was shocked to see the shine of tears in the old man's eyes. "Who are you?" he asked quietly, almost in dread.
A toothless smile quivered on the ancient lips. "Only a maester of the Citadel, bound in service to Castle Black and the Night's Watch. In my order, we put aside our house names when we take our vows and don the collar." The old man touched the maester's chain that hung loosely around his thin, fleshless neck. "My father was Maekar, the First of his Name, and my brother Aegon reigned after him in my stead. My grandfather named me for Prince Aemon the Dragonknight, who was his uncle, or his father, depending on which tale you believe. Aemon, he called me …"
"Aemon … Targaryen?" Jon could scarcely believe it."
And then there is also this quote:
"The gift of a sword, even a sword as fine as Longclaw, did not make him a Mormont. Nor was he Aemon Targaryen."
In total Aemon the Dragonknight is mentioned six times in A Game of Thrones which is by far the book containing the most foreshadowing regards Jon's heritage.
In A Clash of Kings Aemon the Dragonknight again is mentioned six times, and this one quote from Sansa stood out to me.
If Jon's name is Aemon, then just like the Dragonknight he too had an older brother named Aegon, and the two boys had one sister. Rhaenys is of course dead and so there is no love triangle to mirror Naerys and her brothers. But the set of three siblings with brothers named Aegon & Aemon I think is worth noting.
In A Storm of Swords there is another quote which is perhaps one of the biggest hints.
"Every morning they had trained together, since they were big enough to walk; Snow and Stark, spinning and slashing about the wards of Winterfell, shouting and laughing, sometimes crying when there was no one else to see. They were not little boys when they fought, but knights and mighty heroes. "I'm Prince Aemon the Dragonknight," Jon would call out, and Robb would shout back, "Well, I'm Florian the Fool."
In A Storm of Swords there is another quote which is perhaps one of the biggest hints.
Again in Storm Aemon the Dragonknight is mentioned six times and here we have Jon proclaiming it as his own name. This was the first hint that I picked up on that Jon's name may be Aemon and the rest of this post sprang forth from the research I put in after reading this quote and thinking Hmmm, how very George RR Martin to have the boy unknowingly shout out his own name. And I think taken with that quote from Clash where he thinks he was no Aemon Targaryen it fits together very well.
The mentions tail off a little after this with him popping up only four times in Feast, and just the once in dance. But there is another final element to factor in.
Another Babe taken away to hide his identity; from someone who would kill him for his Fathers blood. Dalla's son, a Kings son. Who's mother died to birth him and who was subsequently named by another. As Jon was named Jon by Ned. This baby is named instead by Gilly who gives him the name Aemon.