As today Köningsberg is Kaliningrad and thus part of Russia, this country should be included.
Finally, the only real contoverse is about Vatican City (or rather the entire city of Rome) - and that since the beginning of the HRE! Accordingly, Vatican City should be removed from this list or at least marked as controverse in order to educate the quizzers about this ancient controverse. ;-)
The land area of San Marino consisted only of Mount Titano until 1463, at which time the republic entered into an alliance against Sigismondo Pandolfo Malatesta, duke of Rimini, who was later defeated. As a result, Pope Pius II gave San Marino some castles and the towns of Fiorentino, Montegiardino and Serravalle.
So San Marino should be certainly included.
I will say that my new trophy looks great on the mantle beside 'Contractionist of the Year' and 'If It's Broke, Fix It' :)
HRE article includes several maps, some include the Teutonic Order State, others don't. The "title" map goes over the Slovakian border, others don't and stop exactly on the modern Czech-Slovak border. So Slovakia should be excluded, unless you find a detailed map showing that some village in today's Slovakia actually belonged to the Czech crown at some point.
Let me add https://en.wikipedia.org/wiki/File:Teutonic_Order_1466.png just as an example of a more trustworthy citation of the source.
To put it another way, imagine a quiz that asked for all the countries "controlled by" the United States in it's entire existence, but then the only answer was the United States.
Friedrich II The Kaiser of The Holy Roman Empire was the King of The ''Kingdom Of Jerusalem'' too.