1

I love Regensburg. An elegant city. It is a good reason to go to this part of Bavaria, which is known as Franken. Nice landscape, lots of small and less small beautiful towns and cities.
But there is more in Germany. Last year I went to the north for the chain of old Hansa cities, like Wismar and Stralsund. Top of the list over there is Lübeck.

2

I've been to all the towns mentioned by the OP. I really don't care too much for Heidelberg and Freiburg. My favorite town in Germany to repeatedly visit is Tuebingen, it has it all. Hilly cobblestone streets, half-timbered houses, a castle, interesting nontourist shops, one of Germany's oldest universities, and the nextdoor delightful well-preserved medieval Bebenhausen Monastery. Regensburg is also excellent.

Germany is full of excellent places to visit, after all, there are over 30,000 castles and palaces alone. The centers of the large cities have been destroyed by intensive bombing in WW-II, but in the smaller towns and places in the countryside are many excellent places to visit which may be they purported centuries old dates instead of a post-War rebuild, hundreds or thousands of them. Visiting many of the towns mentioned guarantees that you will be surrounded by hordes of your fellow tourists. while a short distance away will be excellent towns visited by few tourists. Take Rothenburg ob der Tauber, for example. We only usually visit in February to avoid the masses of tourists. Yet nearby are Schwaebisch Hall, Wolframs-Eschenbach, Merkendorf and Vellberg, the latter three having completely walled oldtowns. You'll see few tourists in them. Note that I didn't mention more touristy Noerdlingen and Dinkelsbuehl, also walled medieval towns.

In and around anywhere in Germany should easily be a week or two of excellent places to visit, if not months' worth. Why go to those few places where tourists congregate, when there are equal or better places out there where there will be few tourists at all, and almost no foreign ones? Where you can experience the "real" Germany, interact with the locals, and hear German spoken instead of English, Japanese and Chinese.

3

Greekness, are you planning another trip to Spain, Netherlands, Switzerland, Germany and Czech Republic and are trying to narrow down options of where to go? Or are you asking for people's city ranking as a kind of parlor game?

If it's the latter I guess that's fine, but you seem to imply there are only a half dozen places really worth visiting in each country and it's imperative for us to figure out if small city X deserves to be included in the pantheon. I'm not sure what that gets us. I liked Regensburg, Olomouc, Haarlem, and St. Gallen. I couldn't begin to compare them to every comparable city, but don't see that a trip specifically to any of them would be a bad thing.