The Cinque Terra in Italy is probably the best example.
Im not a big fan of crowds either, but using Ricks guidebooks has helped us have many enjoyable trips to Europe.
there are other places without major tourist attractions (like Paris, Rome and London) or without the idyllic vistas (like the Cinque Terra) that still offer charm and intimacy without the overwhelming crowds.
We have used his guidebooks on numerous trips, especially Europe Through The Back Door, and can recommend the following small cities and towns off the beaten path. Note: theres not a lot to do in these places, a few have small museums or walking tours, but as for shopping, its limited.
His books have details on what to see and where to stay and how to get there.
Colmar, France - near the border with Germany. Has an old church with a famous altarpiece tryptych painting and a little Venice district with canals and winding cobblestones streets.
Stresa, Italy - near the border with Switzerland. On beautiful Lago Maggiore. Cheaper than the more famous Lago Como nearby.
Murren, Switzerland - in the Berner Oberland, surrounded by the magnificent alps. There are other small towns in the area, but Murren is where we stayed. More cows than cars on the road. Trails and funicular railway to ascend to the mountain peaks.
St. Goar, Germany - (not to be confused with nearby St. Goarhausen) a quaint town on the Rhine River. Ruins of an old castle can be toured.
All of these places are just half a days train ride or less apart. If you go during shoulder season (April-May or Sept-Oct) the tourists population should be greatly reduced (its already lower than the big attractions to begin with).
Separate from these places is Scandinavia, especially Norway. Oslo is my favourite big city in Europe. Lots to do there, without the crazy crowds you encounter in London, Rome and Paris (its also more expensive for the most part) The Fjords, especially Naerofjord, are life changing, more breathtaking than Yosemite Valley IMO. Bergen, is also a nice city to visit. Copenhagen, Denmark is another Scandinavian city I would highly recommend. If you dont want to bother with hotels and trains, you can see all these Nordic cities on various cruises. We liked Viking the best (no kids, smaller boat), but also enjoyed our Celebrity cruise.