Breweries in west/central europe

In Plzen, Czech Republic you will find the world famous Pilsner Urquell Brewery. It is worth a visit as is the city. We were there three full days and thoroughly enjoyed the visit.

Easy-while you're in Munich, visit the kellers-the beer cellars of the large breweries that always have seasonal offerings on tap. My favorite is the Augustiner Keller, down the street from the Hauptbahnhof on Arnulfstrasse. They have a large garden too, and the last week of May should be pleasant. If you can, try to get to Salzburg to see the Stiegl brewery. I've never been, but friends of mine have and they loved it. Stiegl is pretty much my favorite European beer. Can't be beat on a hot day. Salzburg is a couple of hours by train from Munich.
French countryside ale is a little less common than German lagers, but still tasty and there might be some small operations near Luzern or Chamonix. Plzen isn't terribly far from where you are, but it's a little out of the way and there are plenty of good options closer to where you will be.

Although there are exceptions, I should probably point out that most brewers in Europe don't offer tours of their facilities to the general public. Too many sanitation and safety issues to make it profitable. However, many (particularly the smaller ones) operate an on-site restaurant or guesthouse. In Munich, of course, the big brewers operate beer halls, the most famous and rowdy example being the Hofbräuhaus. In my opinion, the best brewer in Munich is Paulaner, although their beer hall's a pretty modest affair. I wouldn't use the term "microbrewery" as it applies to the US for Germany. There's about 10-15 national brands, and the rest are mostly regional. I'm less familiar with any of the regional brewers in the areas you're visiting, but should you happen to stray up to my area... definitely check out the Schmucker guesthouse in Mossautal, hidden deep within the beautiful Odenwald region.

Emily: The Grossglockner High Alpine Highway is not anywhere near Milan. The Grossglockner is north of Lienz, Austria, and it comes out just outside Zell-am-zee. And the scenery in the region and over the Grossglockner Highway is simply THE BEST ANYWHERE! You'd do best to take a train from Milan to Verona and rent a car there. Go north on A22 autobahn/motorway toward the Brenner Pass, and right on E66 into Lienz. From Zell-am-Zee, Salzburg would be a good stop, and they have the fine Augustiner beer hall/gardens there. It's run by a monastery and is a favorite. I also agree about Augustiner Beer Hall in Munich. If you're facing the train station, it's to the left on Bayerstrasse and back a few blocks on your left. If you're going toward Fussen, by all means visit the Andechs Abbeyone of the absolutely best monastery beer halls (since 1455.) It's only 28 miles southwest of Munich. Next trip, booking a open jaw flight into one city and out of another will avoid the costs of backtracking and allow you to see more places.
Have a great trip!

Serious beer drinkers love to talk about the brew, as justification to themselves if nothing else. So it's not surprising there are lots of beer blogs. One user-driven site that has piles of information, often up to date, is http://beerme.com/index.php The search function on the right side is the dregs (for a couple of years it thought every brewery was in West Africa) but you can use the regional guide on the left to browse for plenty of thirst-making information. Play around on the Net and you will find more.
Brewery visits, like tours of wineries, get routine pretty quickly. I prefer to search for the pubs that don't serve the international beers you can find back home.