I like Montreal for the overall balance of the skyline. From a lot of angles Toronto is flat and then peak and then flat again. Calgary has a massive cliff and typically the skyline's depth is hidden (from a few angles though I like it better than Toronto, others focus on buildings I don't much like and drop it massively). Vancouver and Ottawa are pretty well a plateau. Montreal to me grows gently to a central point, with enough of an increase to not be a plateau but not enough to make buildings look out of place. I fine Winnipeg also manages a similar overall form. Edmonton is somewhere between Montreal and Toronto for steepness.
I know it's not very qualitative, but I like it when the whole skyline feels like it's working together to create an image. (Though Hamilton and Quebec City's method of ignore any semblance of skyline and just tossing buildings up wherever creates a very unique look.)
And to appease the photo gods: A photo by Chadillac that Google thinks is the #1 Great Canadian Skyline on this website.
Obviously Google has very unique taste.
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