Coming a bit late to this party, but here are my picks:

Must distinguish between Beerhalls (inside places) and Beer gardens (“Biergärten” in German). As to Beer Halls (and restaurants), I have to go with essxjay and the Augustiner Großgaststätte (on Neuhauser Straße just down from Stachus, or up from Marienplatz). Unlike her, though, I also enjoy the Hofbräuhaus for a cool Maß of Helles. Call me a peasant, but there it is.

However, as to Münchner Biergärten, here are my five top picks (and I’ll add a few “interesting” places as well).

1. Augustiner-Keller, Arnulfstr. 52. OK, so I happen to be addicted to that brand, but this particular Biergarten is the quintessential Biergarten. It has *everything* from towering Chestnut trees, self-service and served areas, lots of tables, lots of Gemütlichkeit, and some of the (almost) best beer in town. It is about a five-minute walk from the main train station (Hauptbahnhof) – just follow the street that goes along the right side of the Hauptbahnhof (as you’re facing it), that’s Arnulfstrasse, past the train station, down into a draw (lots of cross traffic) and start up the other side. Off to your right you’ll notice a lot of trees and maybe hear some noise. That’s the place. Or you can take the S-Bahn to the Hackerbrücke stop, go up to the bridge, turn to the north, and the street at the end of the bridge is Arnulfstr. You’re past the Biergarten, so when you get off the bridge, cross the street and turn to your right, go across one cross-street (“T” intersection, actually), and you’re there.

Location used to be the public execution grounds for Munich back in the 1800s, but the last public execution (by guillotine) was 1861, or so I’m told.

While you’re enjoying the beer and atmosphere, if you should get hungry be sure to try the Haxen! It’s the best haxen in any of the biergärten I’ve visited!

2. Biergarten am Viktualienmarkt. This one is in the center of the city, about two blocks from Marienplatz. As biergärten go, it’s not that outstanding, but it is convenient and it has an interesting story attached to it. Unlike most beer gardens that can trace their lineage back to before the wars, this one’s only a couple of decades old. The first time I was there, it was a turn-around station for trams, and when the stop was abolished, the question was what to do with the space (very valuable). Finally it was decided to turn it into a biergarten, and Chestnuts were planted and tables brought in.

This is a popular place for folks working in central Munich to take a break and have lunch (or even breakfast of Weißwurst and sweet mustard – traditionally eaten before 1200 noon). Also, unlike most biergärten there is not a single brewery associated with the beer garden; instead, the major Munich breweries take turns supplying the suds. (There is a sign on the kiosk where the beer is dispensed telling you which brewery’s turn it is today.)

3. Seehaus in Englisher Garten (also mentioned by zzboba earlier in this thread and probably the one bostonbali was thinking of). This one probably has the best location (and is reputed to have the best fresh-baked pretzels) of any Biergarten in Munich. It’s located in the English Gardens up toward Schwabing, and gets its name from being on a small lake (“See”). There are lots of ways to get there (you could take U-3 or U-6 to Münchner Freiheit or Dietlindenstr. and amble from there), but the best way is to walk or bicycle through the English Gardens starting from the Hofgarten next to Odeonsplatz. The English Gardens are the largest urban park in the world, larger even than New York’s Central Park, and are very beautiful. They also, on nice days, attract nude sunbathers, but be warned: not all the naked people are women, and there are some bodies that (not to put too fine a point on it) were designed to be clothed.

4. Hirschgarten (mentioned by USAFAN). This is Munich’s largest Biergarten, located not too far from Nymphenburg Palace, and yes, as the name implies, they have deer here. If you’re walking, take the S-bahn “stem” all the way to Laim, then ask directions. Or, you can walk from the Augustiner-Keller (#1 on this list). It is huge, but service is fast, and it’s well worth the visit. They serve Augustiner, and (sometimes) Helles from the Ducal brewery in Tegernsee, which is also some fine beer! Here are some testimonials, and links to another map and a website.

5. Paulaner-Keller am Nockherberg. I guess the reason I like this one is that it is the location in the Spring for the Starkbierzeit festivities. It’s a little hard to get to (take U-1 or U-2 to Kolumbusplatz, then climb the hill), but the location is really nice. As the name implies, they serve the various Paulaner beers.

And now for some other Biergärten I find interesting:

A. Unions-Bräu in Haidhausen. This is the best beer in Munich <”what?? {gasp} that’s Heresy!”>. Maybe so, but it still is (in my opinion) the best beer in Munich, and that includes the wonderful Augustiner. The beer garden is small, not visible from the street. The Chestnuts are recently planted, and still small (although they are tall enough to provide some comfort from the sun). The main attraction of the Biergarten is the naturally cloudy beer (both blond and dark) they serve. I believe it is made on site, and inside the building you can see the brewer’s equipment. The cellar is also a great place to quaff a cool one, particularly if it’s raining out. A “must visit” if only to try the beer (I’m not impressed with the food, though). There is also a neat Jazzkneipe nearby. NOTE: On 30 November 2012 the Unions-Bräu closed. I don't know if the place was taken over by a different company, or what happened to it; I'll find out later this month when I get back there, and then update this. In the interim, here is a "rememberance" website showing pictures of what the place looked like. Further Update: I walked past the place on May 18th, and although the sign was still up, the door had a notice posted across it saying the business was closed. No idea what they intend for the building. I'll check periodically, and post any developments I become aware of. Sad to see this place close.

To get there take U-4 or U-5 to Max-Weber-Platz; if coming from town (Odeonsplatz) walk in the direction of travel and take the two-way escalator (yes, it’s possible) up to the surface, staying to your right. When you get to the surface, you should be standing right in front of Einsteinstr. 42; the Biergarten is through the building.

B. Hofbräuhaus Biergarten. Yes, they have one, but it’s in an interior courtyard. If you’re going to be there anyway (and how can you visit Munich without at least looking in – it would be like driving through South Dakota and not stopping at Wall Drug), it’s a nice place to escape the Oompah music. I like the tables around the fountain in the middle.

C. Franziskanergarten. A Biergarten like any other . . . except that, in keeping with the “Lederhosen und Bluetooth” attitude of modern Bavaria, it is also a Wi-Fi hotspot.

D. Waldwirtschaft Großhesselohe (also mentioned by USAFAN). Known as "Wa-Wi" (pronounced "Va-Ve"). Also a Biergarten like any other . . . except that instead of Oompah music, they do Jazz. And pretty good jazz at that. Tended toward Dixieland when I was there. This one is well outside of central Munich, toward the South, and along the Isar River. If you’re so inclined, you could ride a bicycle along the Isar to the Biergarten and enjoy a Radlermass (cyclist’s mug), like what the Brits call a Shandy.

E. Forschungs-Braueri. Well outside the central city, but still not too hard to get to. Take S-1 to Perlach and ask directions (it’s just a couple minutes walk from the station). Arguably not truly a “Biergarten”, since there are no Chestnut trees and you can’t bring food with you, but in one way it is a beer drinker’s heaven. There are all kinds and varieties of beers to try here. Watch out for the St. Jakobus Doublebock – it’ll put even a pro under the table in no time (over 18% alcohol, I’m told).

These are just a few of the estimated 400 Biergärten in the Munich standard metropolitan area. Just think how much fun you could have trying them all . . . (Everyone needs a goal in life.)