Here are some suggestions for great day trips from Munich without throngs of tourists.
My favorite is to take the S8 southwestbound to the end of the line at Herrsching. Walk a couple hundred meters to the lakefront and board one of the stately paddlewheel ships which cross the Ammersee to my favorite untouristed Bavarian village, Dießen am Ammersee. Walk through Dießen up to the baroque-rococo Marienmünster Abbey (1730). Return to Herrsching by ship and take a taxi or bus, or walk three miles up a forested trail, to Kloster Andechs, where Benedictine monks have been brewing great beer since the 15th Century. (Photos of Herrsching, Dießen and Andechs here)
Or take S1 about 20 minutes from Hauptbahnhof to Oberschleißheim, and visit the magnificent, colorful Schleißheim Palaces, summer home of the Bavarian royal family. Aviation history buffs will enjoy Flugwerft Schleißheim (aviation branch of the Deutsches Museum), a short walk from the Schleißheim Palaces.
If you have a free Sunday, go to the spa town of Bad Wörishofen, birthplace of naturopathy. Therme Bad Wörishofen is a wonderful spa/sauna/waterpark complex. Then go to the open-air cafe on the small grass-runway airfield on the north side of town and watch skydivers do their thing, while you wait for your 45-minute ride in a classic 11-seat, Russian-built Antonov An-2 biplane (advance reservation required; photos here).
Tourists have yet to discover Ingolstadt, a charming, friendly town about halfway between Munich and Nürnberg. There are many historic buildings in the old center, including the former Anatomy Building of the University of Ingolstadt, now the German Museum of Medical History. Gardens in the courtyard are made up of medicinal herbs and plants. The building was the setting for Mary Shelley's original 1818 novel Frankenstein. Tours are available of the Audi factory, just outside the old center. Ingolstadt self-guided walking tour available here.
