The Beguiling, tucked away in Mirvish Village just off of Honest Ed's, is probably the classiest comic shop in the city. They specialize in the more independent and art-range books, but still carry the superhero stuff too (because even the superhero stuff can be done exceptionally well). The quality-to-floor space ratio is unmatched.
What's also impressive is how well connected The Beguiling is to the comics scene. For a small shop, they have a lot of signings by great talents; for instance, they brokered a charity auction of a Simon Bisley painting on eBay for tsunami relief a few years back. And no, I didn't come close to winning, alas.