Versus is great little spot serving strong coffee. Their popular patio on busy Adelaide St is bathed in sunlight from April to October. Their grilled cheese is delicious but pricey.
I haven't tried Third Wave but it's always busy when I walk by. Seating is limited.
Another favourite in the 'hood is Rooster on King East, just west of Berkeley. If I remember correctly, there are comfortable sofas and club chairs at the back of the space. I haven't been there in a while.
There's also Au Pain Doré on Front, just west of Market St. Their coffee's good and they attract a friendly crowd of all ages and backgrounds and no attitude. Their pastries and sandwiches are good too, if a little pricey. Seating's fairly plentiful.
Neo's very design-y - practical seating seems to have been sacrificed for design purity - the crowd's a little 'tude-y and their food offerings are very expensive, although the matcha log is delicious. The baristas are friendly.
Fahrenheit is great. The baristas are super friendly. There's almost no seating though. It's grab--maybe sit a few minutes if there's a spot--and go.
I'm hoping The Saint, Alias and 88 Queen will offer even more options in the next couple of years.
On a side note, there's an Ali Baba's now on Queen E, just west of Church. I guess it kind fills the hole left by Shawarma's King, which was forced out of the 'hood a year or so ago because of the condo coming to the northeast corner of Queen and Church.