Cantillon is essential if you've never done it. L'Ermitage brewery is nearby, so if it's open you could combine it, though I've never been a fan of their beer. I definitely recommend making the journey out to Brasserie de la Senne. The Brussels Beer Project bar on Rue Dansaert is worth a look. They have a full taproom in the suburbs but I've never been.
For pubs, one of my favourite things to do in Brussels is the Rue Marché aux Herbes pub crawl, starting at A La Bécasse and taking in A L'Imaige de Nostre Dame, Au Bon Vieux Temps and Toone, with the option of going further up to A La Mort Subite. The specialist beer bars I'm in most often are Gist and Moeder Lambic Fontainas, both of which are very central.
If you're seriously into lambic, both 3 Fonteinen and Boon have taprooms and are a short train trip out of the centre, to Lot and Lembeek respectively. Boon has very competitive prices on its high end stuff at the brewery shop, if you're buying.
