Small Town

C/K would be my pick. It's right in the middle of some of my favorite cities, and it's served by some fine shuttle services that can take you between Salzburg, Vienna, Prague and Budapest for reasonable rates.

For a break between big cities, Cesky Krumlov has the smaller-town feel, with only 15,000 population.

I recommend Cesky K. a lot, but maybe I need to pull back a little. I haven't been there in 3 or 4 years and I know the tourist crunch hasn't gotten any better. If you do CK, spend a night to be there when the day trippers are gone. Otherwise your question doesn't have a lot of context so its hard to answer.

Check these out.
Pecs, Hungary
Eger, Hungary
Gyor, Hungary

Sighisoara, Romania
Sibiu, Romania

Varna, Bulgaria
Plovdiv, Bulgaria
Nesebar, Bulgaria

Novi Sad, Serbia

Banská Bystrica, Slovakia
Banská Štiavnica, Slovakia

I could easily spend another couple of nights at any of therse. I guess tops are Sighisoara and Nesebar.

"Or other suggestions please." In which direction? Of those listed, I would say Görlitz.

Other small towns as a place for a night or two to get away from the big cities, totally understandable, I recommend are: in Germany...Weimar, Meißen, Lüneburg, Schwerin, Neustrelitz.

In Austria...Graz, Wiener Neustadt. In CZ ...Brno.

In HU...for me it would me due to historical reasons Györ, Mohacs.

Görlitz, but I'm biased. It's a perfect example of a Central European town, completely preserved with buildings from Gothic, Renaissance, and Baroque to Commie style, which surround the medieval old town like onion rings. The hotels add to the experience. I usually recommend Frenzelhof, a preserved Gothic trader's home from 1480 with a private chapel... it's really like a museum just for you. From Görlitz you could do day trips to Bautzen, a equally beautiful small town with impressive fortifications and a Baroque old town, or the Zittau Mountains. There you could take the nostalgic steam train from Zittau to Oybin to see the romantic ruins of a castle and a monastery on top of a sandstone mountain that looks like a bee hive. And next to the mountain is the wonderful little "mountain church".

Cesky Krumlov. Other suggestions: Halstatt. There are plenty of pretty, non-touristy small towns in A, CZ, D, H, PL. Brno is worth seeing but it is not exactly a small town with 400 thousand people.