Recently, I came across another source for estimating renovation costs at Ontariocontractors.com. The site breaks down the estimated cost of just about everything you might want to do to your home, like roofing, exterior finishes, interior renovations, electrical, HVAC, structural modifications, etc. I am not sure how accurate the prices are, but they seem to be in the ballpark. That said, the site also has a build-a-home calculator that seems to be way out of line with what I have been told so far. The calculator uses a set value of $100/sq ft. to build a new 2-storey house. I haven't heard anyone say it would be less than $200/sq ft.
Other useful items on the site also include a flowchart for general steps to take into account when building a house, although again, the prices they quote seem low. It is also possible to search for contractors on the site, and to post a tender for a job in order to hire a contractor.