Hands down, the absolute best brewery/biergarten I've been to in Germany (or anywhere for that matter) was Weihenstephan in Friesing. The tour is quite interesting and very thorough, and they give you LOTS of beer during the tasting session at the end - complete with some soft pretzels to cleanse your palate. They also have the worlds largest yeast library since it's also a brewing university, which is worth a look if you can. Their biergarten is like something out of a movie. Weihenstephan sits up top of a rather large hill overlooking the small but beautiful town of Friesing, and the view is just majestic. They have hop bines strewn about the seating area, so when the wind blows just right, you can smell the Noble hops as you sip some of the best beer in the world and eat some top notch traditional German food.
I'd love to go back there and bask in the view while sipping some German Pilsner and eating some schnitzel and a sampler platter of various cured meats, sausages, and fermented vegetables. Wife and I went there during our honeymoon in 2009, so hopefully not much has changed since then.
We were not impressed with Oktoberfest, honestly. It's like a big carnival with beer, drunk people, and kids. They still do some of the traditional events that are worth a few pictures, but other than that, it's kind of a mess. As my German friend told me, "Oktoberfest is for drunk Russians and American tourists." It's something to put on the list of things that you've done to say you've done it.