2 weeks in Bavaria region

If you're wanting to visit Octoberfest, you need to find a room now. I would suggest you take a train over to Salzburg for a couple of days. Then you can take a train down to Innsbruck. I would suggest you renting a car in Innsbruck for day trips to ramble throughout the Tirolean countryside. You can also make a day trip into Southern Bavaria, including seeing sights like Neuschwanstein Castle. Innsbruck to Munich can be done by bus or train.

I have already been to Switzerland and Austria

Reuben
My husband and I were just in Bavaria for 8 days and based on that I suggest 1) take train from Munich to Fussen to see Neuschwanstein castle (the Disney castle) and the neighboring (within walking distance) castle, Hohenschwangau - in the bavarian alps and the scenery is spectactular as are the castles. 2) take a train to Regensberg, about 1.5 hours. We did not and I regret it, it is supposed to be beautiful and I think it's a world heritage site. We went to Nuremberg instead (also a nice city), but we went for the Christmas Market. if you are a serious WWII history buff you may like it as there are several Nazi sites there. (along those lines, Dachau concentration camp is outside Munich if you want to tour it). 3) I do highly recommend going to Rothenberg ob der Tauber (about 1.5 hours from Munich) -- it's a perfectly preserved medieval town -- most of the town is original buildings, wall etc. Take the Night Watchmans' tour- fantastic. 4) we did not drive the Romantic road or go through the Black forest, but you may like those as well (West of Munich). 5) we stopped in Wurzburg for a day - there is a large palace and fortress there, it is a lovely city but I would not rank it high on my list. Hope this helps

I just posted this to another question. You should take the train down to Garmisch for a day or two (as the Germans do). There are many options here: walk the towns, train along the valley, train up the Zugspitz, lifts up - hike down, see the gorge. You can't go wrong. If you decide to go down for a night or two, then you can't go wrong staying here: http://www.gasthof-fraundorfer.de/ Get an early train and you will find yourself in a car with hundreds of German hikers and cyclists heading down for the day. From here you can get the valley train to the cog rail or lift to the top of the Zugspitz. But, I would not do this. Instead, head for the Partnach Gorge. It's an easy walk up through the gorge and from the top you can continue up farther to the top of a ski area that has a nice goulash lunch. You can come down via Wamburg, an alpine town. The trails are well marked and you can get a good guide from the TI or from Compass Maps. It's impossible to get lost and bring your camera. http://www.gapa.de/Garmisch-Partenkirchen_Sights_Partnach_Gorge I made this trip with my son and it is one of my most memorable days. If you have a spirit of adventure then you could take the valley train to the Aplspitzbahn lift. This brings you to a beautiful series of alpine meadows. From here you can hike up the Alpspitze or down to the bottom or down to another lift. All are easy to do in one day if you are reasonably fit. Let me know if you want more detail. Here are some pictures of the area:
http://www.flickr.com/photos/jcgannon/5286611007/in/set-72157625536667281/

The first step is to book your lodging in Munich. Availability during Oktoberfest is limited and you may have to adjust your dates. Then you want two towns or villages to stay in before that? Garmisch-Partenkirchen has been suggested as a daytrip from Munich, but we enjoy staying there for three knights to have some time for hiking. The Klamm hikes, the Alpspitze, it is all good. People really like nearby Mittenwald too, be we have not stopped there. Hopefully others can suggest nice scenic places to spend more of your time; I don't have any recent experience beyond Munich and G-P.

Reuben, Munich has lots to offer, read Rick's book for good walking tours. Consider stopping in Dinklesbuhl to the north en route to Rothenburg and Wurzburg for northern Bavaria towns. To the south, you cannot go wrong w/Garmisch as a base (including trips to Mittenwald, Fussen and castles, Oberammergau, Linderhof castle, Ettal monastery). To the southeast, Berchtesgaden and Salzburg. To the southwest, visit Lindau and on to Meersburg. We love this area! In Garmisch, you may want to check out Berggasthof Panorama (family of Frauendorfer) in the Partenkirchen section. Easy parking if you have a car, and easy to walk to Ludwigstrasse shops and restaurants if you can walk hills.

All very good suggestions. This past spring, we spent 2 days in Rothenburg. AND yes the famous Nightwatchman tour is awesome! We stayed at the Garni Hornburg Hotel just outside the medieval walls. We stopped in Dinklesbuhl on our way to Oberammergau. We stayed two days in Oberammergau and used it as a based to see Ludwig's castles, the Wieskirche (absolutely amazing church), Garmisch area, Ruette and climbed up a mountain just outside Ruette to the (just discovered within the last 10 years)Erhenburg Ruins. Just a few other tidbits.

I recommend taking a side trip to Dachau to tour the former concentration camp. It is very somber and enlightening. The train trip is only about 45 minutes from Munich.