Any trip along the Rhein & Mosel is great. Can be done by train & boat too. Bacharach is a lovely little town. Plenty of opportunity for wine tours august to october, and there's usually little festivals on everywhere, easy to look up anyway. Cologne worth a stop off.
Trier is a beautiful small city on the Mosel, near Luxembourg (also a nice small city), with the best Roman ruins anywhere in middle-Europe. Loads of castles can be visited along those rivers.
Bamberg (not far from Nuremburg in northern Bavaria/2 & a half hours from Frankfurt), is a great ancient small city, fantastic beers and bars, and in that region there's also lovely wines, with some good tours. Nearby Wurzburg also worth a visit, and Bayreuth. Not a million miles from there to Leipzig & Dresden.
If you'd like to see the Alps head for Garmisch, can get there handy from Munich or Memmingem (Ryanair flies direct from Dublin). Memmingem itself is a very nice town. Salzburg (just over the border in Austria) is fabulous.
Spa towns ('Baden') are great in Germany, for example, Baden Baden near Karlsruhe (not far from Stuttgart), Bad Homburg (near Framkfurt), Wiesbaden (lovely city near Frankfurt, also has a gorgeous old grand casino), and loads more. Bad Windsheim near Bamberg also very nice.
In Northern Germany Bremen is a lovely city. Dusseldorf also worth a visit.