The Doctor in The Big Bang said he hated repeats. What could he have been scared of repeating? The War Doctor.
The very title, The Name of the Doctor. Fans were in holy uproar that Moffat would give the Doctor an actual name after fifty years of Doctor Who. But the title never had anything to do with the Doctor's given name, but the name he chose for himself. It's all about the name of the Doctor itself. and inferring the horrible thing's he'd once done that made him renounce the name of The Doctor. We were told we would hear "The Name of the Doctor" in the episode and we did, those exact words.
The title of the episode is a perfectly logical reference to the Doctor's greatest secret. After all, if this particular regeneration isn't worthy of being called "the Doctor", what's his name?
In the Expanded Universe, the Great Intelligence is stated to be Yog-Sothoth, an outer god said to exist at all points of time and space. Where the Doctor is concerned, that literally is what it is.
While we later find out there's a somewhat more scientific explanation for the size of the Doctor's tomb, at the same time, it's somewhat appropriate considering that the size of the gravestones on Trenzalore are said to denote someone's position and rank during that final battle. Whoever erected those graves must have decided to leave the TARDIS where it was, finding it fitting that the Doctor's grave should tower over all of them!
Artron Energy is absorbed by all those who travel through the Time Vortex and has been mentioned as causing some physiological changes. The Doctor mentions he's probably experienced the most time travel of anyone in all of history (which coming from a man who's race made time travel their hat, says something), meaning that because of his long-term exposure, his readings must be off the charts! Taking all of this into account, no wonder his "body" is a Negative Space Wedgie!.
When the Great Intelligence was condemning the Doctor for all the aliens he has butchered, it seemed odd that he would miss the Sontarans even though one of them was present. That's because, as a Sontaran, Strax would then have the moral right to deny him, while nobody present had the right to speak for, say, the Sycorax. Why give them that opportunity? Not to mention that the Sontarans wouldn't consider all the deaths their race has suffered at the Doctor's hands to be an atrocity, but noble sacrifices who have fallen in glorious battle with a Worthy Opponent! After all, these are the guys who actually wanted to fight in the Time War and were furious when they weren't allowed to. Sontarans love the Doctor's talent for destruction.
Peace and Sanity are two words that don't get associated with the Doctor.
The Doctor`s fear of Trenzalore, because of his tomb existing there, in addition to the fact that he`s doing something that time travelers should never do. Something that represents his end. As River Song pointed out, the Doctor hates endings. Which is why he (usually)never visits past companions (except, of course, when his 'death' approached him in series 6 and his actual death approached him in The End of Time) out of fear of endings.
Take a look at this line from the Great Intelligence, knowing what we know by the end of the episode.
The Great Intelligence: For me, peace at last. For you, a worldofhurt.
The EU toys with the idea that the Doctor was, in an earlier life (via either being an incarnation before the First, a literal reincarnation, or literally made from his raw material (etc), a Time Lord known as "the Other", who co-founded Time Lord society alongside Rassilon and Omega. John Hurt is literally the Other Doctor!
At first glance, the connection between the Great Intelligence and post-Library River Song's data ghost is easy to miss: they're both literally information manifesting in the physical world, although how they're doing that is a question for another story.
About the prophecy about Silence falling where the Doctor answering a question at the fields of Trenzalore, this might have meant that the Doctor saying his name there would open the TARDIS, allowing the Great Intelligence to enter it and erase his actions from history, causing the retroactive cataclysm we see in the episode.
Thinking back to the Snowmen, Clara being everywhere at once means that she would have seen Eleven with the Ponds. She saw how much he loved them and how broken he was when they died. She knew that word would provoke a response and get him interested in the universe again. Pond. Moffat, you evil genius.
The much-prophezised Fall Of The Eleventh? It's the Eleventh Doctor forcing the TARDIS to fall to Trenzalore.
Clara: How do we get down there? Do we jump? Doctor: Of course not. We fall.
The Doctor's threat to the Vashta Nerada in "Forest of the Dead" is even more prominent if the Library has knowledge of the actions of John Hurt!Doctor. If River Song has access to the same Library, of course she would have knowledge of The Doctor's entire life, hence her behavior in this episode.
The Doctor: I'm The Doctor, and you're in the biggest library in the Universe. Look me up.
Hell, Moffat's been dropping hints at this reveal even before he took over the show. We know he said in the past that there must be some "terrible secret" behind why the Doctor hides his real name. Now we have a hint at the secret thanks to the last few moments of the episode, plus the other hints he's scattered.
Reinette: Doctor who? It's more than just a secret, isn't it?
The Doctor: Good men don't need rules. Today is not the day to find out why I have so many.
In this episode, it's revealed that River's sacrifice has already happened. We don't know when exactly. But remember how depressed the Doctor was in "The Snowmen" episode, after losing the Ponds? Maybe it was more than that. Maybe he's also mourning River Song in addition.
Clara traversed the Doctor's entire timeline, but never once saw John Hurt!Doctor. While this is initially excused as him not being a "Doctor", it makes sense in light of the Great Intelligence's plan. He sought to undo all the good the Doctor did, and this Doc did something so evil he lost the name. Naturally, neither Clara or the Great Intelligence are going to wind up focusing on an act of indescribable evil.
More likely, it was because that incarnation of the Doctor was the one involved in the Time War, which is time-locked. Thus Clara didn't have access to this part of the timeline.
The Great Intelligence may not have had the nerve to try to tackle the Doctor on Gallifrey, which presumably had defenses against tampering with its history even before the Time Lords went to war against another time-traveling species.
Since this episode makes a point of what the Doctor calling himself that means — the name Doctor being a promise — the Doctor's growth and development over the course of the series could be equated to him finding out the answer of the "first question" for himself: Doctor Who? What does the name of "the Doctor" really MEAN?
In the Classic Series, the Doctor's true name is a mystery even to the Time Lords. Given how his name accesses his entire time stream, its no wonder the Doctor has kept it secret from them. Especially when it would allow you to change Gallifreyan history through the Doctor, including the Time War.
Why was Oswin able to overcome Dalek programming? Her need to save the Doctor was so great!
The Silence/Academy are either the biggest group of idiots in the known multiverse, or they are the greatest magnificent bastards in the history of the series. Their whole plan, from The Big Bang on, was predicated on killing the Doctor to ensure he would not make it to Trenzalore.
Option 1: Idiots!: They kidnapped Amy Pond (an act that they should have known was calculated to press the Doctor's Berserk Button) to get at her unborn child, who was part Time Lord. They then kidnapped the newborn, and raised her to be, in the Doctor's words, a "bespoke psychopath", to kill him so that he would never make it to Trenzalore. As befits any Wile E. Coyote-style plan, the complexity is their weakness.River Song falls in love with The Doctor, and at some point down the line, he tells her his name, ensuring that she can be in a position to open the tomb on Trenzalore, allowing the Great Intelligence to monkey with the Doctor's corpse and thereby creating whatever conditions the Silence were so keen on avoiding.
Option 2: Magnificent Bastards!: They wanted all of Option 1 to run exactly like that. Perhaps it was all a sophisticated game of reverse psychology, and the Silence actually wanted the Doctor to get to Trenzalore and things turn out exactly as they did. Why else would the Silence and the Academy seem to be completely MIA after The Wedding of River Song, essentially throwing up their hands in surrender? Why else would there apparently be no "plan B" when the "kill the Doctor with the amazingly convoluted plan that seemed tailor made to present him with an irresistable puzzle" plot went seemingly off the rails?
There are a number of scenes in the Weeping Angel episodes in which the angels remain immobile even when nobody on-screen is looking at them. On first viewing, it makes it seem as if they're over-cautious, or as if the Fourth Wall is being broken and the audience is freezing them in place. But now we know that Clara's splinter-selves have been protecting the Doctor without his knowledge, so the angels' immobility makes sense: she's been peeking at them over the garden wall, out of windows, and so forth from off-camera, paralyzing them just long enough to keep him safe!
Just before the Master regenerates at the end of "Utopia", he foreshadows the revelation of this episode's end when he says: "Still, if The Doctor can be young and strong, then so can I.", thus implying the existence of John Hurt's older incarnation of the Doctor.
Who buried the Doctor? He did. Knowing that his death would leave behind a dangerous Negative Space Wedgie, he prudently prepared an unbreakable locking mechanism, and left instructions for his surviving friends to install it in the tomb they'd build around his timeline. He attuned it to open only in response to his name, then had the TARDIS isolate the chamber where it was kept from her network of corridors, with instructions to make the device accessible in the event of his confirmed and permanent demise.
The Great Intelligence's comments about the Doctor's past being bloodsoaked, which the others cannot believe? In retrospect, he might have been referring to the John Hurt incarnation, which did cross the Moral Event Horizon!
During "The Pandorica Opens", The Doctor is described as being "soaked in the blood of a billion galaxies." While any incarnation of The Doctor may have blood on his hands, no one would go so far as to say any incarnation we'd seen previously, or their sum total, would equal a billion galaxies. What if that's not hyperbole, but the actions of this disowned Doctor?
Hell the very nature of the Great Intelligence's plan! Anyone who's watched the entire original series run alone should know, undoing all the Doctor's good works throughout time would, as Vastra put it "have dire consequences".
Just to name a few:
The First Doctor would have been murdered while inside the tomb of Yetaxa in "The Aztecs". Ending his heroic actions long before he could even preform them.
The Third Doctor would have been caught and killed by The Great Intelligence while out driving Bessie in "The Five Doctors".
The Fourth Doctor would have been assassinated on Gallifrey in "The Invasion of Time". Thus allowing the planet to fall even before the Great Time War.
The Fifth Doctor would have most likely remained trapped in "Arc of Infinity". Leaving no one to stop Omega.
The Seventh Doctor would have most likely fallen to his death in "Dragonfire".