As the creator of PDFClerk I use most of its functionality at least some of the time, if for nothing else, at least to test it works correctly.
As a PDFClerk user the most important features for me are joining several PDF files together (often printed directly to PDFClerk through the print services menu, from either a browser or a source code editor) and the standard 2 page imposition to create booklets. I either fold them, or may take them to a print shop and have them cut and bound. For creating the booklets I often find myself quickly adjusting the margins in the Document Settings panel, as well as sometimes numbering or re-numbering the pages with the “Relabel Selected Pages” feature in combination with the “Page Labels” settings in the Document Settings panel. When printing from a browser I often find I want to delete the last page, so that is another PDFClerk muscle that is regularly exercised.