Andrew Coyne has his most recent column online, which has a rather simple suggestion.
Since property taxes are neither simple nor fair, why not just get rid of them? He explains this with some detail here:
Municipalities could make up the difference with user fees and sales tax, he says.
I think he's on to something but it might need some refinement. After all, commercial entities would not be paying sales taxes sufficient to pick up their share -- or at all, if it is a GST-style tax. But at the moment I can't think of a single good reason to keep property taxes in Ontario.