Learn English – When does a locational distinction change its suffix and capitialization in a proper name

Proper nouns should name specific people, places or things - "specific" being the key word here. In some cases specificity is immediately apparent, e.g. in the term "Singapore Airlines" (after all, there is only one airline with that name!).

In other cases, there is a grey area and I would say that fame/notoriety also plays a role in determining specificity. To use your example, one would refer to the Guantanamo letters if they don't contain any content that is particularly newsworthy. If, on the other hand, these letters happen to disclose some salient information that could result in a political scandal, then these letters would quickly garner attention and become intimately linked to this political scandal in the minds of people. Such a link would imbue the letters with a specific quality that would warrant the use of a proper noun, i.e. the Guantanamo Letters.

Thus, some common nouns can become proper nouns over time as they gain specificity in the minds of people. This can be a very organic process that can leave plenty of room for interpretation as to whether something should be considered a proper noun or not.

I think that the correct answer to this is refer to your style guide, e.g., APA, MLA, IEEE, SPIE, etc. These should fully specify details like this, and you only sometimes get lucky and have a real human address specific concerns like this (viz., the APA link).

In contrast to what @bib suggests, the APA reference requires that you include a comma between the first name and the suffix:

Doe, John, Jr.

(Also please note that the gentleman's official name will have a comma in it: John Doe, Junior or John Doe, Jr..)