I am looking for a complete list of German states - i.e. lordships,
countships, duchies, imperial cities (Reichsstadt) etc -

and their dominant religion (catholic, protestant) 

for the two years

a) 1555 (Peace of Augsburg, http://en.wikipedia.org/wiki/Peace_of_Augsburg)
b) 1648 (Peace of Westphalia, http://en.wikipedia.org/wiki/Peace_of_Westphalia)

Koenigstadt - aka Kaliningrad

Half of Poland would do

Königsberg ... not Koenigstadt.

I stand corrected - faulty memory and a UK keyboard :-}

Funny how Prussia was Protestant, yet its Eastern domains were Catholic

If Scriptor-ga looked at this question and couldn't answer it or
didn't suggest that he could for a better price, I fear that is is
very difficult.

Probably it touches a nerve.

From my little knowledge the place was a patchwork of religions.

I fear that indeed the question is more difficult than I thought.
I am happy to increase the price if that helps...

It is indeed a complicated matter.  I assume that you have some
background knowledge of subject and maybe read some German, and have
looked at the full text of the Peace of Augsburg (can be clicked on at
the bottom of the Wikipedia site).
At the end of the intriguing treaty, you will see all the people who signed it.
Perhaps they are sorted by Protestants and Roman Catholics, but I
couldn't tell (not that there is any reason that I could).
Frde-ga is right, Germany was a great patchwork of principalities as
the high resolution map for 1648 that you can click on at the bottom
of the other Wikipedia link shows.

I lost the link to a map that showed the religious affiliations of the
parts of Westfalia in 1806(?) which would have demonstrated the
problem of listing Protestants and Catholics for all of Germany in
1648, when the map was more complicated.
This link lets you see how Germany was (dis)organized in 1789:
http://www.hoeckmann.de/geschichte/nrwhist.htm

This is no help, just a little explanation of the problem.