Most people tend to apply to U of T St. George Campus, Queen's, Waterloo, Western and Guelph (not all of those schools mind you, although some people do!), but it really depends on what you want to major in, whether you want to do a co-op, how much scholarship money you'll be offered and whether you can see yourself spending the next four years of your life there!
Quite a bit of people also tend to apply to Ottawa too, because of the scholarships they offer, but I'm sure that the program that they offer isn't bad either.
Also, a lot of people tend to get hung up on the title of the program without really looking into the actual courses you take in the program. This is especially true for all of the med hopefuls who limit themselves to programs named "biomedical sciences" or "health sciences", when really, programs at other schools named life sciences or even biology offer you most of the same courses in your upper-years. The first year in terms of courses you have to take will be very similar at most universities.
So, my suggestion to you is to check out the curriculum of each program, especially the courses they offer in upper-years. BUT, don't forget that things change, and you may not even end up pursuing the program you thought that you would in high school, so choosing a school with a variety of science programs could also be beneficial! And, lastly, try and visit the schools that you are interested in to get a feel for the campus and student life.