More in geographic order west to east than anything else:
1) Tofino, BC
2) Vancouver, BC
3) Okanagan valley, BC
4) Takkakaw Falls, BC
5) Moraine Lake, Banff National Park, AB
6) Columbia Icefield, AB/BC border (best from Athabasca glacier, AB)
7) The Alberta badlands - Drumheller, AB
8) The open prairies of SK (although admittedly, you get tired of it quickly)
9) Anywhere on the arctic tundra, but Churchill, MB makes for a good location to see polar bears.
10) Algonquin Park, ON
11) Niagara Falls, ON
12) Montreal, QC (specifically the old port area)
13) Quebec City, QC (any part of the old city)
14) Tadoussac, QC (whale watching is great here)
15) Any part of PEI
16) Bay of Fundy, NB
17) Peggy's Cove, NS
18) The Cabot Trail, NS
I just realized that you may not be familiar with the provincial abbreviations, so I will try and help out:
BC - British Columbia
AB - Alberta
SK - Saskatchewan
MB - Manitoba
ON - Ontario
QC - Quebec
PEI - Prince Edward Island
NB - New Brunswick
NS - Nova Scotia
Sorry, but Newfoundland and Labrador I have not been to, so I cannot make any recommendations there. I tried to give a list of the highlights of Canada, but if I had to choose my absolute favourite spot, it would be Moraine Lake, Alberta. If you are travelling through the mountains again, try stopping off at Ainsworth Hot Springs near Fraser BC as that is amazing - not beautiful from the outside at all, but amazing once you're in there.
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