sorry--may not have seen this thread in time for your trip, but hopefully can help others who may be headed here. I recently was on a trip to Munich and Prague, and was not disappointed.
In Munich, the biergarten culture is central to the Bavarian beer experience. Seating is family-style, and prepare to sit with other patrons. If your German is ok and/or their English is good, it can be a delightful experience to get to know the locals, who we found to be very warm. My wife and I probably tried the helles and dunkels for the 6 major area breweries, and all have slight nuances that make it worthwhile to seek out. Best spots--definitely go to the biergarten in the center of the Viktualienmarkt, a block or two south of the Glockenspiel plaza. You can find any delicious fresh food at the numerous stands, and then sit down at the biergarten and try whatever beer they serve (the breweries rotate through). The Augustiner garten about 3 blocks west of the train station is also a must-try--absolutely beautiful, and big. Note there are numerous Augustiner locations, but this was our favorite, and the favorite of many locals. The Paulaner brewery has a nice biergarten, and also served the best food that we had in Munich. The Hofbrauhaus is mainly a tourist attraction, somewhat expensive, but worth checking out for the experience. The beer and food were good.
I had an idea of what to expect in Munich, but Prague was a pleasant surprise. Czech beer is more than Pilsner, and also more than the "cerne" or dark style that the major breweries offer. You will find pilsner and cerne anywhere you go. Two stops worth checking out: (1) Klasterni Pivovar, a brewpub near the monastery right above the castle. Typically at least 3 beers on draft. When I was there, the 3 were amber, dark, and a Bavarian weissbier. The amber and dark were more within the czech style, although unfiltered. The weissbier was good as well. They were getting ready to put an American-style IPA on draft, and I wish I could have tried their interpretation. The other (2) is Pivovarsky Klub, about 100 yards east of the Florenc bus station metro stop. A little out of the old town but walkable and very worthwhile. 200 beers available, mostly from artisanal czech breweries. Great food and beer. There are a lot of nuances in the dark style, and you can see and taste for yourself here as this is the focus. This is a style we don't see much (if at all) in the US, and I highly recommend experiencing it, particularly if you like beers that are sessionable. This blows the lid off session beers. One was a lot like the good flavors of smoking a cigar--without the acrid/smoke, just the tobacco goodness. Wow.
Haven't been to Brussels in a few years, but you can't go anywhere without bumping into good beer. If you have time, go just outside to the countryside and visit the lambic breweries. I didn't get to do this but it is highly recommended by others.