I've been to quite a few comic shops in Toronto - maybe a dozen or so - and The Beguiling is certainly my favourite one. They have an unmatched offering of "non-mainstream" comics and comic-related literature which covers the first floor. I've had non comic book loving friends come into the shop with me and tell me they liked it because it felt like a book store, instead of an exclusive environment.
The second floor of the shop is where superhero comics and manga live. They have as good a selection of these things as they do of indie comics on their first floor.
The staff itself are always friendly and willing to answer any questions you may have. They may seem like the "too cool for you" type, but trust me, that's not true.