Yes, it is true. The noble Lord Stannis Baratheon (this was before his ascension to the throne after the death of King Robert and the beginning of the Usurpers' War) investigated thoroughly this matter, which included personal visits to many bastards of royal blood and long nights in the archives looking for historical descriptions of various offsprings of Baratheon-Lannister marriages. Through empirical analysis, Lord Stannis concluded that the royal Baratheon blood was exceptionally strong (I believe some research on this will soon be published by Maester Merol of Riverrun, so keep an eye out!) and that any children from Robert's marriage with the snake-queen Cersei should result in children with black hair as well. As we all know, the witch Cersei was also notoriously involved with various men, ranging from the low, such as the fool Moonboy, and the slightly better-bred, the evil Kettleblack brothers, as well as being known for her closeness with her kingslaying brother. In the circumstances, it was natural for both Lord Stannis and Lord Eddard to conclude that Joffrey, Myrcella and Tommen were all abominations born of incest. This suspicion was confirmed by later events, but I can't really talk about it due to the 20-year rule and the fact that the latest volume of the comprehensive history covering this period has yet to be published.
Joffrey Baratheon was indeed an illegitimate child. You see, there's a genetic difference between humans and the Andals. For us humans, the fact that Robert Baratheon has black hair probably wouldn't be a valid reason for illegitimacy, because Robert could have a recessive blond hair allele that could be inherited to Joffrey, combining with Cersei's allele and generating only boys. But on a barbaric society like Westeros had, the Andals developed a new kind of allele, the complete dominant allele, an allele that destroys the recessive allele and splits itself.
Let's use Robert Baratheon's father as an example, Steffon Baratheon. Steffon's mother was a Targaryen, so we can safely assume she only had blond or silver hair alleles. Now, Steffon's father was a Baratheon, and the Baratheon's seed is strong, meaning they have a complete dominant allele. So, when a child is produced from Rhaelle Targaryen and Ormund Baratheon, the black hair allele from House Baratheon will not only mask Targaryen's blond/silver hair allele, but will destroy it and replace it. Meaning that Baratheon's child will always have black hair.
Of course, you must understand that Mendelian genetics was not developed by the time of the War of the Five Kings, so Westerosi people wouldn't know for sure about it. So Stark propaganda indeed had a great effect on people's beliefs.
Given that both Baratheon and Lannister sources are so heavily compromised this is unfortunately outside of responsible historical speculation. What can be said is the effect of these accusations, which were widely accepted, particularly in the Riverlands and Crownlands. This greatly hurt the legitimacy of Joffrey I and Tommen I, and undoubtedly contributed to the popularity of Brotherhood movements in those regions.
Oh boy, this one is controversial. As I'm sure you are aware, the question of King Joffrey's legitimacy was the main justification for the War of the Five Kings. I say justification, because all but the most biased sources will acknowledge that the political situation in Westeros had become untenable long before the birth of King Joffrey. I'll avoid going into any real detail on the background, but there has been a great deal written on it. In particular I recommend Maester Tarly's History of the Baratheon Dynasty. Some consider his status as an oathbreaker to compromise the work, but I think on the whole it is an unbiased account.
With that out if the way, the answer is we really don't know. Jon Arryn understandably kept few notes of his secret investigation and it has been argued that the rivalry between House Stark and House Lannister compromised Lord Eddard's findings. Furthermore, Lord Eddard's father was rumored to have had ambitions to secede, and Lord Eddard may have been looking for justification. King Robb I provides more evidence for this by showing how readily the northern lords embraced independence.
This is getting long so I'll leave you with my opinion. The strongest argument that King Joffrey was a bastard is the testimony of Stannis Baratheon. Yes, there is obviously great cause to question his objectivity, but his reputation for honesty is without peer. It isn't indisputable evidence but I do not believe Stannis would prepare such a fraud on Westeros.
The claim that Joffrey I Baratheon is the incest-child of the king's wife and a knight of the Kingsguard is so absurd that I am astounded that respectable historians accept it as anything but a justification for a rebellion in the North.
There are plenty of situations where even Targaryens had heirs lacking the silver hair and purple eyes that defined the dragonlords. Yet, where were the accusations then? Some rumors of course, but no rebellion over it.
It is clear that the Eddard and Catelyn of Houses Stark and Tully sought a justification to declare independence from the crown, now that the Targaryens had been ousted and Robert I Baratheon, Mother keep his soul, no longer present to keep his friend in line.
An excellent question! For quite some time, this was a highly contested topic between historians interested in that period. Indeed, the quandary is clear given our primary sources on the topic. They are Queen Cersei Lannister, Lord Eddard Stark, Pycelle, and Lord Stannis Baratheon (as he outlived both Joffrey and Tommen, whether or not Stannis can be referred to as King has been questioned. In this scenario, he is treated like Viserys Targaryen, known as the Beggar King and brother to Queen Daenerys I, and not given the title, rather than King Robb Stark, the Last Wolf).
Each of these four, aside from being profoundly compromised, are known to be of terrible moral character.
Lord Stark was a traitor and sought the throne for himself (many historians suggest that he believed he deserved the throne after Robert's Rebellion).
Lord Stannis also rebelled against the throne and by the accounts of Lord Davos Seaworth (Lord Davos was a tragic figure who was by all accounts a great and honorable man bound to the wrong leader. His crimes were absolved posthumously after suspicion that he had been magicked into service, as was true for many who followed Stannis and his concubine witch, Melisandre) had used foul sorceries to murder his own brother and blame Brienne of Tarth, the first female member of the Kingsguard, for Renly's murder.
Queen Cersei was accused and declared guilty of crimes under numerous powers before being sentenced to death by Queen Daenerys, a well recorded trial that included lengths of testimony against her character that have been well corroborated.
Pycelle, the only Grand Maester to have been posthumously stripped of his rank, is reviled by historians for letting his Lannister biases (it's widely assumed that he was bought off, as he lacked any familial ties to the family) taint his work to often irreparable extents. He passed away before seeing justice (though he was once sent to the black cells by Lord Tyrion Lannister), uncovered accounts make him implicit in the deaths of (among others) Lord Jon Arryn, King Robert Baratheon Queen Margaery Tyrell, King Jaehaerys, at least one High Septon, and even more of a traitor to King Aerys than Jaime "Goldenhand" Lannister, the man who slew Aerys to save the city. He accomplished these murders not with a blade, but by dispensing knowingly poor (and sometimes explicitly harmful) advice and medical care.
Indeed, even science fails to help us. Rudimentary genetics of blonde as a recessive trait may suggest the accuracy of Eddard and Stannis's claims, but as we discovered the complexities of genetic inheritance and expression, the matter became quite inconclusive.
Fortunately, however, the matter has since been resolved in recent years thanks to the preserved wisdom of King Petyr Baelish the Savior (also known as the Peacemaker, the Wise, the Regent, etc).
After marrying Queen Daenerys to unify the realm in her name (then merely Lord Baelish, though he only ruled the Riverlands, the Westerlands, Vale, Iron Islands, and North were very loyal to him and his judgement, as he had protected, rescued, and returned to power the rulers of each), Our King set about ensuring that the story was set straight for what occurred in those chaotic years. After Queen Daenerys tragically fell in battle against the Others, King Baelish then took leadership himself at the urging of all other leaders in the Seven Kingdoms.
When he made peace with the White Walkers, one of the secret terms of the deal was that they be caretakers of a tome assembled from the notes and journals of maesters and knights and lords across the realm, including those of Lord Varys, a noted spymaster, and King Baelish himself. This tome was assembled in such a way that it told the true history of the times leading up to those events, detailing everything from the tail end of King Aerys II's reign to his marriage to the end of the War of Ice and Fire, the last chapter being those very negotiations. In his great wisdom, he asked that the book not be returned to human society until a century after his death so that the wounds we had inflicted on each other could heal.
And so, in the fifteenth year of King Gregor Martyn's reign (as you all know, King Baelish never took another wife after the death of Queen Daenerys, and thus never had any children. He abdicated before his death, so to avoid the wars he had seen in his younger years, and established the new precedent of a non-hereditary and instead meritocratic monarchy when he chose Queen Sansa Stark as his successor, which continues to this day), an envoy from our northern neighbors returned this book to us. Scholars have been pouring over it since that date. Though it a more popularized version has made, King Baelish's true version remains a critical text for historians both as the definitive history of those times, and as the greatest display of how to gather and collate historical sources into a cohesive text.
And so, from this great gift from our wonderful King Baelish (may he rest in peace and continue to look after us all), we have our answer.
Yes and no. Joffrey, Tommen, and Myrcella were certainly illegitimate, but they were not the result of an incestuous pairing between Cersei and Jaime.
Though there was a union between the two in younger days (in the days when Jaime Goldenhand was vulnerable and still wracked with guilt over his Kingslaying, before King Baelish first came to court and helped him through the crisis), the timing of it does not corroborate with the conception of any of the three. Instead, however, the two boys are the children of Stannis, while Myrcella is the child of Ned. Stannis fathered the two during his time as Master of Ships, while Ned did so during the Greyjoy Rebellion. This is why both felt secure in their claim of illegitimacy, as they knew firsthand of that fact.
Unfortunately, after the Others attacked King's Landing, Joffrey Baratheon's corpse, along with thousands of other corpses dead and buried, rose from the grave, and were destroyed by dragonfire during Daenerys Targaryen's liberation of the city. It is therefore not possible to exhume Joffrey's body to perform a genetic analysis.
Archaeologists continue, however, to scour the ruins of the Red Keep, for something, anything – even just a hairbrush or a scrap of clothing – which might provide some closure on this issue.
In some ways, the question of Joffrey Baratheon's actual legitimacy is beside the point.
The War of the Five Kings was, in actuality, a continuation of the War of the Usurper. The Arryn-Stark-Baratheon-Tully (and, eventually, the Lannister) Alliance was too weak to survive the challenge to it's legitimacy, fracturing before it had coalesced into a solid governing coalition. For instance, the Arryn-Tully portion of the alliance was broken by Jon Arryn's death and Lady Lisa Tully's seclusion. Robert Baratheon's death, followed so quickly by allegations of incest, fractured the already strained Lannister-Baratheon alliance, while infighting amongst the Baratheons over the succession cost them dearly. The Tully-Stark portion of the alliance was the only one working in concert with one another, but the Red Wedding severed those ties permanently. Lingering in the background throughout all of this was Daenerys Targaryen, the Targaryen Pretender to the Throne of Westeros and the Mother of Dragons.
Whether or not Joffrey Baratheon was legitimate or not is, in some way, beside the point.
If the accusation was enough to topple the newfound dynasty, it wasn't strong to begin with.
It is clearly stated so many times by either Jaime or Cersei that Joffrey was their child. I have no idea what the hell you're arguing over. Perhaps the question was meant to be more on the "was the throne his to sit on" side. If we look at the picture as a whole, Baratheons had no claim to the throne besides their Targaryen ancestor. IMO though, Aegon simply united the 6 kingdoms under his rule, but isn't that usurping as well in a way? Because as far as I know not all the kings besides Torrhen Stark were happy to bend the knee.
What a loaded BS question. I can't stand guys like you. Stark propaganda? Really? I think if you're being honest with yourself you know that the Lannisters (and let's face it, regardless of his last name is, Joffery is a Lannister) pretty much corner the market on propaganda in Westeros. Let me guess the rise in poverty in King's Landing is the Starks fault too? Sorry, I know this is a history question but I had to say something given the clear bias of the questioner.