Kakashi has the left eye and Danzo has a right eye Sharingan, so it's quite reasonable that a greedy old ninja like Danzo went after Toby's right eye.
Madara has his right eye still too and I thought his little brother was supposed to have died upon giving up the eye so it's likely just Toby's right eye.
It's also possible he took Tobi's
left eye and implanted it into his right eye socket. Remember, Tobi's eyehole is on his right side.
Though the chances of that working is highly unlikely since I don't think the left hemisphere of his brain (the side of your brain that works in tandem with the right eye) would be compatible with a left eye.
But meh, it's a possibility nonetheless.