How do I... decide with DTD to use
is there any prons/cons in using html, xhtml with different DTD's?
For HTML, DTDs are almost entirely irrelevant, unless your personal workflow depends upon DTD validation. For XML, DTDs can still be necessary to define character entities like &alpha, which are not predefined like in HTML.
To clarify, Prince will not even load DTDs in HTML documents. It will load DTDs referenced in XML documents, and use them for entity definitions and fixed attributes. Note that this can require repeated HTTP requests if you refer to DTDs that are not found locally in the Prince DTD catalog.