In Brussels you have to go see Cantillon, anybody who works there will talk about beer all day, the more questions the better. It's where I fell in love with gueuze. Don't mind all the spider webs, there's a rhyme and a reason
If you have time and are willing to make the trek, it was absolutely amazing to go to Westvelteren. It's a days worth of traveling to and from Brussels, and much easier if you have a car, but possible by train/bike. I took the train to Poperinge and then walked (yup) each way to and from the abbey. Beautiful scenery along the way, including hops.
I'm going to second everything BK said. While I was in Köln my favorite was
Früh, in Dusseldorf it was
Uerige, but you really can't go wrong anywhere in either city. Also, in Köln a neat place was the chocolate factory, and I was a fan of all the above ground water main.