Thinking back about Tobi's battle with Konan, he used Izanagi to escape from Konan's ultimate technique! I searched through blogs and Narutopedia but couldn't get the source of his left eye, that he used to overcome Konan's ultimate technique.
Although it is not explicitly stated as such, he supposedly gathered several Sharingans during the Uchiha incident.
This "cupboard" in the room where he operated on Sasuke is probably where he preserves his "collection". He has been showed standing next to it on one or two other occasions.