Why did Kaneki's nails turn black?
His nails turn black because his nails died and the blood, below his nail, were trapped there and dried.
By repeatedly cutting off and breaking Kaneki's limbs, Yamori had inadvertently strengthened Kaneki's kagune to far surpass his own. The torture resulted in Kaneki's hair changing from black to white because of the increase in cellular tubes in his RC cells in his kakuho, thus increasing his own RC cell count.
“Blood… my skull is split and I taste honey.” (Haise, :re Chapter 53) Kanae repeatedly kicked him in the head, he cracked his skull and that's why his hair is covered in blood now. Most Mangas have a black-and-white style, so his hair has shown to be black because of the blood.
Kaneki's white hair - caused by extreme emotional/mental stress when tortured by Jason, again not really an explanation needed here but I would like to note that kaneki's hair is now permanently white, it can't revert back to its original colour.
1. Ken Kaneki. As the hero and main protagonist of "Tokyo Ghoul," it makes a lot of sense that Ken Kaneki would also be the strongest character in the series.
Ken Kaneki cracks his fingers as a consequence of a traumatic torture cycle brought upon him by Yamori. He does not break them, only cracks them. It symbolizes his duality and is the pinnacle of his “transformation” into a one-eyed ghoul, which occurs before and during fighting an opponent.
Ever since his mother died, Kaneki has developed his personality to resemble his mother's. He despises the idea of solitude, hence he tries to protect those dear to him so he would not have to face his fears of being alone in the world. This is perhaps his greatest weakness and act of selfishness.
1. Eto Yoshimura (One-Eyed Owl) Eto is probably the most powerful ghoul in the series. In the guise of the One-Eyed Owl, she was able to fight and kill several Special-Deputy Rank Inspectors, causing her to be classified as an SSS Rank Ghoul.
That's especially important for the series' protagonist, Ken Kaneki, a half-ghoul whose left eye is that of a ghoul, which he keeps hidden from his human friends. When Kaneki inevitably gets a ghoul mask, it's one that inverts the “mask” he has to wear as a human; it blocks his human eye and exposes the ghoul eye.
Kaneki had to heal his toes over and over again, all the while being tortured and practically starved. His body was basically weakening because the cells were wearing out, which is why his hair turned white, as it does with individuals as they age. Torture is also why Takizawa from Re: had his hair turn white.
Why did Kaneki start cracking his knuckles?
Kaneki started doing as a result of Yamori always doing it when he was torturing him, and Yamori picked it up from the human investigator who tortured him. Naki also does it, on a different finger as a tribute and to mimic Yamori."
Hide lets Kaneki eat his face to get back his strength. While it appeared at first that Hide had died in the process, he reappeared later as Scarecrow, an ally of Kaneki and the ghoul hunters.
After becoming a half-ghoul, Kaneki's right eye changed. His sclera became pitch black, but his pupil became a bright shade of red. His other eye remained a dark grey, however. When people think of anime characters with two different color eyes, Kaneki is certainly one of the most popular ones.