The Manx Pub on Elgin St. is excellent and has very good food. It has a selection of microbrew and imports on tap. The only issue is that it can be very hard to get a table.
Across the river in Hull, there's a new brewpub called Brasseurs du Temps that I've heard good things about.
I have to recommend The Highlander in the Byward Market area. It is a traditional Scottish pub that has numerous single malt Scotches available, plus the full compliment of draught and bottled beers. The owner is a character. I can't say if it's the best pub, not having been to many in Ottawa, but the Highlander would certainly be worth a visit, especially for Scotch drinkers!