Oh man I saw the reply just now, anyways, I got an anwser per note from L-Tenshi. I will post it here for ya ^^
"I think the reason his nails are black is due to him being hit with something heavy (like a hammer) in the fingertips.
If you ever hit yourself with a hammer by accident it turns it black as the blood is becoming old under the fingernail. In some cases the nail might come off however maybe due to Kaneki being a ghoul his regeneration prevents that.
Hope that answered your question, albeit the answer might be a bit brutal-ish."