What are the best multi-day hikes in Canada?
There are several. Definitely the Rockies (Banff area in Alberta) offer some of the best, but I believe the absolute best is the West Coast Trail in BC. It is in bear county, so you have to be "bear smart" in the summer, but it is one of the best multi-day hiking experiences in the world.
http://en.wikipedia.org/wiki/West_Coast_Trail
Enjoy!