Depending on where you are, BrewPub is a good centrally-located, er, brewpub (Adeptus reviews it here[/url:sjot1nky]), but if you can get to Nørrebro do. Look out for bottled Nørrebro in other bars and shops, likewise Mikkeller and Amager beers. Ølbutikken is the best beer shop in the city, if you can take beer back with you.
Unless you really don't have time to go elsewhere, Apollo and Vesterbro brewpubs can be skipped.
All locations can be found on BeerMapping[/url:sjot1nky].