The same thing occurred with my recent YOW-SEA flights. I ended up saving $30-40 (and those are real, Canadian dollars, not that monochromatic play money) by booking two One-Way tickets.

The bottom line is that it is worth it to spend the few extra minutes on trans-border flights to check it out a couple of different ways. There may be other benefits, as well (it took me four tries to figure out how to get ac.com's booking engine to route me SEA-YVR-YYZ-YOW with the transcon segment on the red-eye).

Of course, reading Shareholder's post above, I wonder if travelling out of an HST province (for example, YHZ-YYZ return), it would be cheaper to book that as two O/W's as well, in order to save HST on the return?