Most online ebook stores will gladly sell to Canadians. I've gotten books from Fictionwise, Booksonboard, Shortcovers and eBooks.com without any issue.
If you're interested in French language books, you might be interested in hearing that Archambault has recently open an (ePub) ebook store:
Jelis.ca. Their catalogue is rather small now, but they're only just starting...
If you want an english language ebook store store for "Canadian Content", however, I don't think I've seen any of that yet (but I have to admit I haven't really looked).