I was just in a little town called Marken not far from Amsterdam. It's a bit touristy but very pretty. You can take a bus there from the city. Find out more here: http://wikitravel.org/en/Marken
The neighbouring city of Monickendam is lovely as well. about 6 years ago
Marken is on a peninsula and unique to The Netherlands but not your typical small village ;-)
Utrecht we consider a city. Very nice with a lot of canals and old city center but different from Amsterdam.
Very pretty and not invaded by tourists are: De Rijp, Giethoorn, Schiedam, Zaltbommel, 's-Hertogenbosch, Elburg, Amerongen, Zierikzee etc.
If you are looking for a private local guide who can take you to these places and show you the country side meeting the locals go to: www.holland-is.com
If you like more information on The Netherlands, follow my new blog http://www.netherlandstravelexpert.com/ almost 6 years ago