There was an article about pubs on Saint Jean Street in Bieres et Plaisirs, Oct 2009. In French, but you'll get the gist:
http://journal.bieresetplaisirs.com/arc ... _10-09.pdf
I went to Quebec City a few months ago and tried several of the pubs in the article. I really liked Bateau de Nuit. It's a dark and dingy, but the owner is super friendly and was willing to talk to me about Quebec beers en francias. He has a few books on QC micros at the bar in case you need a conversation starter. Some hard-to-find QC beers on tap. There's a separate article on this place on page 2. Based on my single visit there, BdN seems to pick up after 10pm or whenever the local punk band shows up to play.
Lots of tatoos and probably a near-complete line-up of Unibroue at Ninkasi. Busy if there is a game on.
Sacrilege didn't have a whole lot on tap, but you'll feel like one of the locals if your able to get a seat and sip your Cheval Blanc in the tiled, back-patio-like area.
A trip to the Corsaire is always a good idea, but it is probably best in the evening so you can see the lights of the city from across the river. And if you miss the ferry, you can always go back for another pint.
La Barbarie is downtown in the Lowertown area on St. Roch. Since they don't have food, you might consider duck confit pizza at Mo's Urban Tavern around the corner on Saint Joseph for dinner. (There are some amazing bakeries on St. Joseph if you in the area during the day.)
If you have wheels, the brewpub on L'Ile d'Orleans is about 30 minutes away. It has a very nice view of the river, and you can see the Montmorency Falls on the way there. Don't pay for the cable car. Just drive to the top.
Also for people with cars, Depanneur de la Rive is a must if you're looking to fill up your trunk and break some laws regarding interprovincial transport of alcohol. It's a dep that sells QC micros and basically nothing else. Floor to ceiling beer.
If you don't have a car, there are a couple of stores along St. Jean with good selections. Also, try the market in the Old Port. See ads in the PDF.
Not so impressive: L'Inox. Nothing wrong with the look and feel of the place, but their beer tasted like my first homebrew.
On a non-beer-related note, Paillard on St. Jean is a fun place for breakfast or lunch.