Well, if the definition of "truly great" is "consensus world-top 50" than I am fairly confident in saying there are no truly great courses in Canada. Especially given that there are only maybe 20 courses that are consensus world top-50.
Looking at the GW lists, these are the nominees:
ModernThe National GC of Canada - Always ranked among the top-3 courses in the country, this George/Tom Fazio design as an absolute brute. Very comfortable routing over a hilly piece of terrain very close to Toronto. There is a real sense of isolation on each hole. Tremendous hole variety is sometimes over-shadowed because of the course's difficulty / maintenance meld. Recent changes have taken the few breather holes and made them extremely difficult - a poor change in my opinion. A very good golf course, with few, if any, obvious faults. No way it is truly great.
http://www.nationalgolf.ca/Devil's Paintbrush - One of the better faux links efforts I have seen, complete with fescue tees/fairways, nasty pot bunkers, shots played over stone walls and extreme greens. Again, very good, but no way it is truly great.
http://onegolferstravels.blogspot.ca/2012/02/devils-paintbrush-golf-course-review.htmlRocky Crest - This may be my favourite modern in Canada, but the corporate feel (even though it is cottage country) and the dubious conditioning keeps off of the top-lists of some. A phenomenal routing through large areas of lake/wetlands/ large rock formations, though there is perhaps too much emphasis placed on elevated teeing positions. A great example of simple strategic design in an exceptional setting.
Beacon Hall -
http://onegolferstravels.blogspot.ca/2012/01/beacon-hall-golf-club-review.htmlMuskoka Bay Club -
http://onegolferstravels.blogspot.ca/2012/02/muskoka-bay-club-course-review.htmlSagebrush - Haven't seen it. Matt Bosela's Tour:
http://www.golfclubatlas.com/forum/index.php/topic,41154.0.htmlCoppinwood - One of the best Fazio's I've seen, but he doesn't have anything consensus top-50.
http://onegolferstravels.blogspot.ca/2012/02/coppinwood-golf-club-course-review.htmlClassic - If Canada has anything that it truly great it is one of its classic courses.
Highlands Links - GCA's own Ian Andrew has been working on restoring this Stanley Thompson design for the last couple of years. Haven't seen it, but it may be the course with the best chance of being described as truly great.
http://www.highlandslinksgolf.com/Hamilton (Ancaster) - Of the courses I've seen in Canada, this one has the best chance of being world top-50, but not in its current form. If restored I believe that this course would deservedly place amongst the world's best. Current bunkers feel small in scale, many bunkers have been lost over time (and some poorly placed ones added) and the mowing lines are among the worst I've seen.
http://www.golfclubatlas.com/forum/index.php/topic,44318.htmlSt. George's - Another Thompson work that has recently been restored by Ian Andrew. I have not seen it in its current form, but even before the restoration I felt it was the best golf course in Canada.
The following I haven't seen but could be in the running...
Capilano -
http://golfclubatlas.com/forum/index.php?topic=38375.0Jasper Park Lodge -
http://www.golfclubatlas.com/courses-by-country/canada/jasperpark1/