Bad Dog (assuming the new owners still sell the same brand) - hands down, best coffee in the city. Organic, fair trade.
Cafe Don Jorge (Colombian coffee at market) - a very close second, and significantly cheaper by the pound than Bad Dog. Organic, fair trade.
PAMs (at King and James) - consistently good, and great staff.
Bailey's - excellent coffee, nice pub-style interior with low, intimate tables.
Courtyard Cafe - nice flavour, but they need to serve it hotter.
al Centro - very good coffee and cappuccino, but like the Courtyard they need to serve it hotter.
Freeway Coffee House - Very good coffee and a huge selection of teas.
Speakeasy - the batch I bought tastes a little burnt, but otherwise pretty good.
Locke Street Bakery - I can't stand Seattle's Best, so yuck (but their bagels are great and Peter & co. are very friendly).
Starbucks - I think they make the coffee as horrible as they do so you're forced to buy a seven-dollar soy green tea latte venti instead.
Tim Hortons - tolerable if you have it there and get it in a mug rather than a take-out cup.
Second Cup - I can't even abide the first cup. Bleagh.
EDIT - three more places:
Denningers (Jackson Square location) - surprisingly good - much better than I expected.
Deco's (also in Jackson Square) - meh, it's Mother Parker's.
Bread & Roses (at Sky Dragon Centre) - pretty good, but a little on the harsh side.