And the Justice Department says it is investigating whether it might have been an act of domestic terrorism.
It said in a statement, the shooting was "designed to strike fear and terror into this community", and the department was considering all possibilities.
A woman who identified herself as the daughter of Ethel Lance said: "You took something very precious from me. I will never talk to her ever again.
"I will never be able to hold her again, but I forgive you. And have mercy on your soul."
Anthony Thompson, a relative of Myra Thompson, told Mr Roof to repent and to turn to Jesus Christ.
"I forgive you and my family forgives you," he said.
The judge set Mr Roof's bond at $1m (£630,000) for the weapons possession charge but could not place a bond on the murder charges due to a legal technicality.
Mr Roof will now remain in jail, at least until a high court sets the bond for the murder charges.
This was Mr Roof's first court appearance in South Carolina since the shooting on Wednesday night.
He is accused of opening fire on a bible study group, killing nine people.
The state's governor has called for him to face the death penalty.
- 1) Cynthia Hurd, 54
- 2) Rev Clementa Pinckney, 41
- 3) Rev Sharonda Coleman-Singleton, 45
- 4) Tywanza Sanders, 26
- 5) Ethel Lance, 70
- 6) Rev Depayne Middleton-Doctor, 49
- 7) Susie Jackson, 87
- 8) Rev Daniel Simmons Sr, 74
- 9) Myra Thompson, 59
RIP
