Rhaegicide

Viserys Targaryen

I highly doubt it's coincidence that this birth defect has thus far been shown exclusively within the Targaryen family. Whether this is because of Targaryen genetics influencing fetal development is unclear, but doubtable. After all, a significant part of fetal development is dependent on the mother, and Maegor the Cruel's wives (Harroway, Costayne, Westerling) were not Targaryens. Maegor's seed was said to be cursed, but in this case it was admitted as poison.

More likely this is a case of a poison that is known within the royal family as a method to cause deformed stillbirths. Tyanna of the Tower, a Pentoshi woman, was the first known user of this poison, but from there it could have been passed down, or perhaps it is a combination of Targaryen genetics and poison. Either way, Viserys is more likely than most others to know the identity of this poison, being himself a Targaryen prince.

But Viserys is as mad as Aerys II. He is hot-headed, jealous of his sister Daenerys, and scornful of her husband Drogo. He wants his due from Drogo, and is not giving it. Is that enough to kill his sister's unborn child? Perhaps. His temper and paranoia seem to be exacerbated by Daenerys's pregnancy. He may very well have been deluded enough to see Rhaego as a threat to his claim. This, combined with his scorn for both Daenerys and Drogo, could have motivated a poisoning.

Lastly, let's consider where Viserys directly threatens Daenerys, in Daenerys IV, AGOT:

Viserys scrambled back to his feet. “When I come into my kingdom, you will rue this day, slut.” He walked off, holding his torn face, leaving her gifts behind him.

Now obviously Viserys never does come into his kingdom, as he dies in Daenerys's next POV chapter, but it could well be that he decided to poison her in the days between this point and his death. But if it was Viserys who both conceived and executed this plan, how would we find out about it? The bread crumbs seem a bit too well-placed for this to be something we never see confirmed in the text; I find it far more likely that someone alive either did the poisoning or the planning, or perhaps both, or else there may be no realistic vehicle to reveal such knowledge to the reader.

Mago or Jhoqo

Mago and Jhoqo are honorable mentions for this theory for a couple very weak reasons: they are still alive and will appear again; and they had a clear contempt for Daenerys during her tenure as Drogo's Khaleesi. With regards to their reappearance, we can defer to GRRM himself, when he speaks of the show's killing-off of Mago:

So Mago is not dead in the books. And, in fact, he’s going to be a recurring character in Winds of Winter. He’s a particularly nasty bloodrider to one of the other Khals that’s broken away after Drogo dies.

The khal to whom he refers is Jhoqo, whom Daenerys encounters in the final chapter of A Dance With Dragons. GRRM's note that Mago will be "a recurring character" could mean either that Mago joins Daenerys if and when she steals Jhoqo's khalasar (unlikely, as bloodriders are required to die with their khal regardless of how he dies), that Jhoqo follows Daenerys (unlikely, given his clear contempt for her), or that Daenerys travels with the khalasar for a few chapters before taking it from Jhoqo.

During this period, it could very well come out that one of the two had Daenerys poisoned during her pregnancy. Daenerys already has sworn them a painful death after their rape and murder of the Lhazareen girl Eroeh. What more vengeance could they ask for by admitting to poison? Not much, but even if they decided to push that button, what would make Daenerys or the reader believe them? Not much, which makes one of these two a possible candidate, but an unlikely one.

Jorah Mormont

Ser Jorah Mormont has been in love with Daenerys since the very first book, but not since the very first page. There was a time when Ser Mormont cared only about a pardon from Robert Baratheon and the leave to return to Westeros. When word gets out about a lordship for the lives of Viserys and Daenerys, he stops the wineseller that attempts to poison Daenerys, but who's to say he didn't slip her something else later, something that would only kill her son?

I admit that this is unlikely, and if it was Jorah it was likely due to being expressly manipulated for this exact purpose. But there is yet one more thing against this, that being the history books of Westeros he gifted Daenerys at her wedding, most of which she has yet to read, in Daenerys II, AGOT:

Ser Jorah Mormont apologized for his gift. “It is a small thing, my princess, but all a poor exile could afford,” he said as he laid a small stack of old books before her. They were histories and songs of the Seven Kingdoms, she saw, written in the Common Tongue. She thanked him with all her heart.

Surely one or more these books contain details of the poisoning for Maegor the Cruel's wives, or details of Rhaenyra Targaryen's suspected poisoning during the Dance of the Dragons. Perhaps they don't spell out the poisoning, but if Daenerys had read those books she would have spotted something familiar about her own miscarriage. Now, Jorah isn't the brightest bulb on the tree, but is he dim enough to try poisoning Daenerys after giving her the very means to discover what happened? Perhaps, but I'm not so sure. I do thing Jorah was part of this plot, but not knowingly, as I'll detail with the final suspects.

Illyrio Mopatis & Varys

These two are the most compelling suspects for this. They were not present for the poisoning by any stretch of the imagination, but I believe them to be the core conspirators of the event.

As we learn in A Dance With Dragons, Illyrio and Varys are supporting the claim of Rhaegar's son, Aegon VI, not his sister Daenerys. Illyrio seems to be giving both Daenerys and Viserys a lot of support in A Game of Thrones, but it later comes out that he didn't even expect her to survive her time with the Dothraki, let alone to hatch dragons. The purpose of Drogo was to sew chaos in Westeros, and weaken it for invasion by Aegon VI. This is discussed face-to-face between Varys and Illyrio in Arya III, AGOT:

“Perhaps so,” the forked beard replied, pausing to catch his breath after the long climb. “Nonetheless, we must have time. The princess is with child. The khal will not bestir himself until his son is born. You know how they are, these savages.”

The man with the torch pushed at something. Arya heard a deep rumbling. A huge slab of rock, red in the torchlight, slid down out of the ceiling with a resounding crash that almost made her cry out. Where the entry to the well had been was nothing but stone, solid and unbroken.

“If he does not bestir himself soon, it may be too late,” the stout man in the steel cap said. “This is no longer a game for two players, if ever it was. Stannis Baratheon and Lysa Arryn have fled beyond my reach, and the whispers say they are gathering swords around them. The Knight of Flowers writes Highgarden, urging his lord father to send his sister to court. The girl is a maid of fourteen, sweet and beautiful and tractable, and Lord Renly and Ser Loras intend that Robert should bed her, wed her, and make a new queen. Littlefinger... the gods only know what game Littlefinger is playing. 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. And now his wife has abducted Tyrion Lannister, thanks to Littlefinger’s meddling. Lord Tywin will take that for an outrage, and Jaime has a queer affection for the Imp. If the Lannisters move north, that will bring the Tullys in as well. Delay, you say. Make haste, I reply. Even the finest of jugglers cannot keep a hundred balls in the air forever.”

What ever came of that? What haste did Varys or Illyrio ever put into getting Drogo to "bestir himself" sooner? If his son is dead, he may go. As with Rhaenyra Targaryen, poison to induce a stillbirth may get him going a month or more sooner, and a month is more than they had before. What's more, Varys makes sure there's a very public poisoning attempt via the wineseller, conveniently foiled by Jorah, to make Drogo suspect that Robert caused Dany's stillbirth and march on Westeros. In fact, when Drogo learns of the wineseller's attempt, he vows to march on Westeros for vengeance. From Daenerys VI, AGOT:

When Dany told him what had happened at the market, all laughter stopped, and Khal Drogo grew very quiet.

“This poisoner was the first,” Ser Jorah Mormont warned him, “but he will not be the last. Men will risk much for a lordship.”

Drogo was silent for a time. Finally he said, “This seller of poisons ran from the moon of my life. Better he should run after her. So he will. Jhogo, Jorah the Andal, to each of you I say, choose any horse you wish from my herds, and it is yours. Any horse save my red and the silver that was my bride gift to the moon of my life . I make this gift to you for what you did.

“And to Rhaego son of Drogo, the stallion who will mount the world, to him I also pledge a gift. To him I will give this iron chair his mother’s father sat in. I will give him Seven Kingdoms. I, Drogo, khal, will do this thing.” His voice rose, and he lifted his fist to the sky. “I will take my khalasar west to where the world ends, and ride the wooden horses across the black salt water as no khal has done before. I will kill the men in the iron suits and tear down their stone houses. I will rape their women, take their children as slaves, and bring their broken gods back to Vaes Dothrak to bow down beneath the Mother of Mountains. This I vow, I, Drogo son of Bharbo. This I swear before the Mother of Mountains, as the stars look down in witness.”

Drogo vows to do exactly what Illyrio and Varys want him to: march on the Seven Kingdoms. But as Illyrio points out, he won't make any moves until Rhaego is born. Varys says they need make haste, so how can they do that? Induce a miscarriage. Poison Daenerys and make her pregnancy end sooner, so Drogo will begin his march sooner.

But how would Varys and Illyrio know which poison to use? Well, that's easy. First, Varys served Aerys II for years. He knows more about the Targaryens than most living characters in these books, so he is likely to know which poison caused the birth defects for the children of Maegor and Rhaenyra. What's more, Tyanna of the Tower, the first (and thus far only identified) user of this poison for this type of stillbirth, was a Pentoshi woman. Illyrio Mopatis lives in Pentos, and Varys spent a significant part of his younger life there as well.

But who actually did the poisoning? Viserys was as stupid as Joffrey Baratheon and paranoid as Aerys II. It would be nothing to feed lies to him, making him suspect his sister's child would threaten his claim. But more likely is Ser Jorah, who had a direct line of communication with Varys and Illyrio. He would certainly be too ashamed and afraid to admit this to Daenerys later on, after he has decided his loyalty, and the logistics are most convenient for getting the order out.

But how will we find out about it if it was indeed Illyrio and Varys who conspired it? Both Varys and Illyrio are still alive, and especially with Tyrion bound to cross paths with Daenerys again, she is guaranteed to find out whom Illyrio truly backs for the Iron Throne. And Daenerys is on a course to get that confession personally. From The Queen's Hand, ADWD:

“He’s not wrong,” Ser Barristan said. “What did Prince Quentyn promise the Tattered Prince in return for all this help?”

He got no answer. Ser Gerris looked at Ser Archibald. Ser Archibald looked at his hands, the floor, the door.

“Pentos,” said Ser Barristan. “He promised him Pentos. Say it. No words of yours can help or harm Prince Quentyn now.”

“Aye,” said Ser Archibald unhappily. “It was Pentos. They made marks on a paper, the two of them.”

There is a chance here. “We still have Windblown in the dungeons. Those feigned deserters.”

“I remember,” said Yronwood. “Hungerford, Straw, that lot. Some of them weren’t so bad for sellswords. Others, well, might be they could stand a bit of dying. What of them?”

“I mean to send them back to the Tattered Prince. And you with them. You will be two amongst thousands. Your presence in the Yunkish camps should pass unnoticed. I want you to deliver a message to the Tattered Prince. Tell him that I sent you, that I speak with the queen’s voice. Tell him that we’ll pay his price if he delivers us our hostages, unharmed and whole.”

If this promise is truly to be fulfilled, and Daenerys is to be involved in fulfilling it, it is reasonable to infer that by invading Pentos (where Illyrio lives), she will once again encounter Illyrio. With the knowledge that Illyrio backs Aegon VI, whether from Tyrion or from rumor, Daenerys is bound to question everything Illyrio has ever done for, as Jorah has rightly warned her to do in the past. This would be prime opportunity for GRRM to reveal the poisoning that deformed Rhaego.