Interesting thread topic. I found myself thinking of this recently too. I am biased I know, but I think in Canada it only comes down to two: Calgary and Toronto.
Vancouver's setting is incredible, but the collection of buildings that make up Vancouver's downtown are fairly nondescript. They certainly
have great buildings and some
world class projects underway, but for the most part their best buildings aren't big enough or prominent enough to stand out. I think the most common skyline I'm accustomed to is the view from North Vancouver and the only building with sufficient character for me to snap my fingers and go "Ah, Vancouver!" is the ferry terminal, and that's understandably low on the horizon. Even before our recent wave of blue glass beauties, I still would have given the tilt to Calgary over Vancouver. Suncor (then Petro-Canada), the Bankers Hall towers and the Calgary Tower and Saddledome especially as a pair offered a look that screams Calgary. Vancouver would be lucky to have any one of those. Calgary has since built heavily upon that baseline, so nevermind the Bow, EAP, Brookfield and Telus Sky . The day will certainly come that Vancouver gets some landmark architecture. When that happens, I'll be ready to reevaluate my opinion as openly as possible. For now, I consider it a fairly distant 3rd.
Montreal is fourth, but I feel like I have room to grow my appreciation. For one I've never been there to see it in person. It does have some more distinct towers than Vancouver to be sure, but Vancouver's setting has to count for something. It's not just what you build, it's where and how you build it.
Quebec City and Ottawa are home to some truly elegant buildings that any city would be lucky to have (Parliament, Supreme Court, Chateau Frontenac, etc.), but these are generally small parts of small cities. At best they cut a dignified air, but to me they're not
skylines in the same way that Toronto, Calgary, Montreal and even Vancouver are.
It was nice of you to include Edmonton and Winnipeg, but they're really not in the running. Edmonton, will have more to speak for it in a few years from now, and the river valley certainly has it's appeal. Winnipeg has some outstanding turn of the 20th century architecture that should make the rest of Western Canada more jealous than most of us know. I think if you're familiar with these cities you can identify them, but otherwise they could be collections of grey boxes anywhere on the continent.
That leaves what I might call the big two. Let's begin with the obvious, TO has not just an impressive skyline, but a globally recognizable one. It has the biggest, the most and certainly much of (but not all of) the best large skyline defining towers in the country. It's intimidating competition, but to some degree, Toronto's scale obliviates it's constituents. The Toronto skyline view,
we all know the one I'm talking about, effectively boils down to three elements. Skydome (nuts to Rogers on the naming matter), the CN Tower and then a mass of other structures encircling them. A lot of the best stuff is in that halo, but it just doesn't stick out. Calgary's smaller size on the other hand does it some serious favours. It's much easier to resolve key elements like the Bow and Suncor in Calgary than it is to do the same for First Canadian Place and Scotia Plaza in Toronto. Some of Calgary's lesser known buildings like Canterra are also given their chance to shine as a result. Calgary is also blessed to have more than a single definitive view. Scotsman's bluff has been the angle of choice for decades and Crescent heights is now well caught on too. The western, further northern and south aspects are also very appealing in my opinion. The hilly terrain and lack of natural obstructions gives Calgary more 360 appeal than any other city on the list.
All told, I have to give it to Toronto on account of it's iconographic quality, but I think it's close between Calgary and Toronto these days. Especially with how Calgary has grown in the last 10 years.
Of course, it's all biased. It's just my opinion, not a equally informed or in any way educated one at that. If I'd been to and spent more time in all of the places on the list I might have more to say in defense of the others.