As I don't have much in the way of Ontario roots these are not sites I've looked at previously.
Upper Canada (Ontario) Criminal Database
Database indexes prison registers from Toronto, Whitby, Guelph, Woodstock, Chatham, Cobourg, Kitchener, Windsor, Peterborough, Lindsay, Owen Sound, Brockville, Belleville, Picton.
Upper Canada (Ontario) Insane Asylum Registers
Insane asylum database indexes to Toronto, Kingston, London, and Malden Insane asylums 1840's through 1900.
Here's a tip. Even if you think your ancestors were never criminal or insane, click and scroll down for additional Ontario databases from researcher/compiler Michael Stephenson.