Brussels:
+1 for Moeder Lambic Fontainas it is kinda near Manneken Pis and on the way to Brasserie Cantillon there is even a walking tour map that Cantillon has on their website with cool stuff on the way from the grand place to the brewery.
For a bottle shop I went to De Biertempel on the northern side of the grand place - had a huge range of beers, even westvleteren range (got the 12 for 12 euro) probably cheaper places but this had the best range closest to the action.
BrewDog Brussels is alright too if you are hankering for a hoppy beer, also is close to the Centraal train station.
Bruges:
+1 for De Halve Maan Brewery I did the XL tour, a bit longer and you got 3 beers at the end, unfiltered Zot, tripel and quad.
Duvelorium Grand Beer Café in the market place, views of the market place and Belfort from the balcony.
Ghent:
A less touristy version of Bruges.
The local gruit brewery was in the process of moving when I was there Gentse Gruut but plenty to be had in the cafés etc.
Het Waterhuis aan de Bierkant (Waterhouse on the Beer Side) a cool small beer café on the Leie River.
Düsseldorf and Cologne:
Go to the centre of old town, walk into a pub, they will all have the same beer (Altbier or Kolsch, depending on city) each pub/café will serve a different brewery. You might be able to order a pils as an alternative. They make good beer but I got bored with the beer selection in Germany compared to the selection at even chain restaurants in Belgium.
Amsterdam:
If you are with non-brewers the Heineken brewery is a fun couple of hours, you wont learn much but I still enjoyed the games etc they had in there.
Prague:
Lokál Dlouhááá a good restaurant, serves beer from the tank.