Growing up in Germany and Switzerland the biggest suggesting I have for traveling through Europe is don't bother with a car. After parking and gas its going to be a lot more expensive then using public transport and nowhere near as convenient.
www.bahn.com
^use this for city to city in Germany
then every major city has their own transport network, here is the one for Munich
www.mvv-muenchen.de
For navigating Germanic cities there is always a Haubtbahnhof ("Main Train Station") in every town/city, it will be marked by a capital "HB" sign. Then there is almost always a Banhof Strasse ("Train Station Street") that the station is either on or the road dead-ends at. If you get lost just look for the "HB" signs that and you will find maps and potentially someone who can speak English.
Most cities have some sort of multi-day / multi-ride ticket for the center of the city, if you really know where you want to go and what you want to see then using local deals for the public transport can be cheaper then the europass; especially if you are not doing a lot of city-to-city or cross boarder travel.
The other really annoying thing for planning foreign travel is how google filters the search results based off of your ip location. Since I can, I search in german and have google only give me results in german that is the only way to get accurate results that isn't just tourist crap. Especially when searching for privately owned and smaller hotels.
if you dont mind very no frills accommodations there is something called a "pension" in German which is typically just a room with a bed and a bathroom. they are usually nice and clean but have no other extras so food and concierge is all on you.
The other thing to search for are "Ferienwohnungen" which literally means "vacation home" or "vacation living space". Typically these are privately owned houses and apartments that people rent out for certain times of the year. Growing up this is typically what we used when we traveled since we liked the space for a family of 5 and the ability to cook when we wanted to.
if you use this site
www.deutsche-pensionen.de you can search by city for cheaper accommodation.
A few quick tip for eating in Germany, unless blatantly stated you can typically seat yourself especially at beer gardens its usually only the really busy ones that will seat you.
Start eating your food when the server brings it to you. A lot of times in busy beer gardens they will bring the food out as it comes off the line rather then when all of the food for the table is ready. This is because of bench style open seating there may be three different parties at single a table and the food is just going to whoever ordered it. So the general rule is "eat before the food gets cold and your beer get warm." If you wait for everyone at your table to be served you may get asked if there is something wrong with your meal.
and when you go to pay if you say "bezahlen" vs "zahlen" you mean you are paying with cash.
The SWMBO and I along with another couple will be spending a few weeks in Germany this summer. We are flying into Frankfurt, but from there we are unsure of what to do. We haven't decided yet where to fly home from either. The only stipulation we have is that everyone wants to see the Alps. I know many of you live in or have lived in Germany or make frequent trips. We're not really interested in tourist traps but also don't want to miss seeing anything that would be worth visiting. Any and all suggestions are appreciated. Thanks in advance!
If you all want to see the Alps then Munich isn't a bad city to base your self out of; there is tons to do just in the city and you are between 2-4 hours on the train to most of the central Alps. (Its about 4 hours on the train from Munich to Zurich.)
The Zugspitze is a cool mountain to visit since the German Austrian boarder runs through it.
zugspitze.de
Like any mountain you go to in the Alps it has great hiking in the summer, and there is always a beergrarten / gasthause that is reachable on a day hike
. This is one of the more touristy mountains in the summer but pretty much every mountain that has skiing have tons of marked hiking trails (Wanderwege) for the summer
www.wanderbares-deutschland.de/wanderwege/wanderwege-karte.html
Even in the cities you will see paths marked with little yellow or white signs typically with a rough distance or time on them, these mark your wandering ways so use them accordingly.
If you want to see something a little different, in Bergtchesgaden there is a canyon called the Almbachklamm where there are tons of waterfalls over over around 3km of bridges, tunnels and cliff side paths. The mountain run off is so clean you can just drink out of the little falls that cross your path.
www.berchtesgadener-land.com/de/almbachklamm-wanderung
there is also an old salt-mine there you can now tour that has giant wooden slides for moving through some of the caverns, for a school trip it was a lot of fun and something different since the mine was started in the 1500's.
www.salzzeitreise.de
As for visiting breweries there are tons everywhere you go; however you usually have to contact them to book a tour or visit so just plan for that.
As others have said Oberramagau is beautiful to visit
Saltzburg is beautiful but the center of the city can be kind of touristy.
Ravensburg is a cool city that sill has parts of the medieval city wall and their gates in the city center.
Schloss Schleishein is really stunning and off the beaten path in Munich
http://de.wikipedia.org/wiki/Schlossanlage_Schlei%C3%9Fheim (it was like an hour bike ride from where I lived outside of munich)
Englischer Garten in Munich is great for a relaxing afternoon in the sun just don't bother going to the beer garten in the middle at the Chinese tower (its a trap).
The Munich Olympic park is is really nice, almost always has some event going on and is right across from the the BMW museum.
there are a lot of really ridiculous Schlossren (Estates, think like Versailles) in Germany, here is a list of all the castles and Schlossern in Germany organized by state
http://de.wikipedia.org/wiki/Liste_von_Burgen_und_Schl%C3%B6ssern_in_Deutschland
Munich also has a high number of art museums with the two biggest being the Alte and Neue Pinakothek. Each would take days to go through.
if you know and like "Der Blaue Reiter Groupe" then the Lenbachhause is the place to go and not too big for an afternoon
www.lenbachhaus.de
Munich also has the coolest natural history museum i have ever been to. it has a stunning car collection, a glass suspension bridge built into the bridge section, a multi-story mine for the mining section and the electricity section has a 300,000volt 1000amp Tesla coil that they simulate lighting strikes with.
www.deutsches-museum.de
These are things i can think of at the moment to give you a solid start on the planing.
My final word of advice is dont try to visit too many cities. It can take a couple days to get your bearings in a new city and trying to do the less touristy things means you have to be willing to just walk the city and go get lost.