I think there is a distinction between what residents vs. other Canadians see as the most iconic building in the city. For most Canadians it might be one or two buildings if any that stand out in their mind as iconic. Here's my perception combined with what I think would be a BC viewpoint:
Victoria: Parliament buildings or Empress hotel. Perhaps the whole inner harbour in general?
Perception by
Irish Fernandez, on Flickr
Pano-Victoria from the Rock by
Cameron Knowlton, on Flickr
Those are all I can see non-Victorians being aware of, locally iconic there's a bunch more including the new Johnson street bridge, Hatley Castle (X-Men and others have filmed here so it would at least be recognizable by some although unlikely to know it was in Victoria), Craigdarroch Castle, the pink Custom House, Christ Church cathedral, yadda yadda.
One that should be up there nationally, is the gates to Canada's oldest chinatown:
The Gates of Harmonious Interest, Chinatown, Victoria by
Jim, on Flickr
Vancouver: Lions Gate Bridge, BC Place, Canada Place
Edmonton: Rogers Place - the tv coverage helps for recognition. Provincial Legislature
Calgary: Saddledome (the Rogers Place of its era - definitely iconic. Makes me wonder if stadiums lose their iconic status after a few decades though) and Calgary tower. The Bow for those who have visited in person.
Regina: Provincial Legislature and the twin office buildings
Saskatoon: For BC, or Victoria at least, this city is totally off the mental awareness map. Regina stands out because of the football team, provinicial capital, there are reasons to travel there from Victoria - but there is no real connection at all to Saskatoon. If you ask most people about it - word association, they would say "berries". Despite being a beautiful city there is no awareness - no one goes there for a holiday and the economy is not linked at all to the island economy. Some would be able to place the Delta CN Hotel.
Winnipeg - great pictures previously shared in this thread, so many interesting buildings!
Despite being further away, much greater awareness of Winnipeg in Victoria, helps being a larger city. The Human Rights Museum for sure, followed by the legislature. Lesser known would be the Forks Bridge, Fort Garry.
Toronto: CN tower, Blue Jays stadium (whatever the corporate name is now).
Montreal: Habitat 67, Notre-Dame, and Olympic Stadium. Montreal has so many great historical buildings that they tend to get lost in the crowd, like Toronto so many high rises that would be icons in 95% of all other cities, but don't even raise an eyebrow in their city.
Saint John! Yes Saint John, visited there for the first time this spring, what an amazing city (skyline shots do it no justice) - would put it in my top 5 of all Canadian cities. It has to be Trinity Church as someone else previously mentioned - it's magical and draws in. A smaller church perched on a small hill, you're drawn to it like a magnet - so inviting.
Halifax: Purdy's Wharf - they are looking dated now, but they do stand out on the water, so very recognizable. Clock tower - that would not be remotely iconic for people who haven't been to the city and don't recognize it's significance.
St. John's: No building stands out, other than the overall image of the harbour, the colourful houses and the houses hugging the rocks. I think it has a strong overall iconic image out here, but more a case of the whole is greater than the sum of its parts.
Edit: oh yah, Ottawa! Well, obviously there is just one, but again lots of great historic buildings that in a smaller city would be stars.