Montreal is a really good place to be. I'll be heading back up next Sunday for school. There are several places that are "Must tries" as far as I'm concerned. Smoking is illegal in bars, only really seedy places will have smoke rooms in the back.
JVD X mentioned Brutopia is on Crescent street, which has alot of other bars that are...meh... Brutopia brews their own and I've never had a bad time drinking there. Whatever you do DON'T go there on a Monday, they have live music every night except Monday's when they do trivia competitions or whatever, the guy running the thing thinks he's an MC at the academy awards or that he's Dane Cook or something. Their live music is usually good.
Next, give Benelux a shot. It's located at Sherbrooke and Jeanne-Mance. If you're feeling like taking it light on the wallet hit it on a Wednesday night because that is two for one pint night (still 7.75, ouch) but these coming weeks it will be PACKED as we are all coming back to school (woohoo!) No clue what they have on tap right now, they brew all their beers and its alot of fun.
If you fail to hit either of those, a must go to bar is Dieu du Ciel. This bar will be less swamped with students because it is away from the downtown area. They have awesome beers, huge selection, and everything is fairly strong! You cannot miss this bar! Dieu du Ciel!
Some people recommend Les Trois Brasseurs. Its a chain, its all over the city, I've always had a "meh" experience there....
hmmm... I'm missing a few.... There are plenty of places on Crescent and St. Laurent and all the way up and down St. Denis (a great place for food is L'Academie, on St. Denis, BYOB) that have decent beer and good atmosphere, but expect ALOT of drunk kids at anywhere popular for the next week because McGill Frosh will be going on, as well as regular back to school shenanigans. Down by the waterfront will be alot less crazy as it's a trek and its expensive. Very expensive. I'll be willing to chip in more advice if you want! Have a blast!