PDFs are convenient since they retain the layout of the orginal document, but not if the user doesn't have the right fonts and you don't embed them.
File sizes can be big, so like with graphics, optimizing PDFs for the web is important. I found the smallest PDF sizes can be achieved by using graphics at the size and quality you need before making the PDF. Use less fonts, or only standard fonts, then you don't need to embed them.
Layout and design need to be different if the PDFs are intended for printing (e.g. as booklets) than if they are intended for screen reading.
Some degree of copy protection can be built-in to PDFs, but as usual it is easy to get around it if people really want to.
Larger PDFs can be compressed a little with a good archive program, but it is usually more convenient to leave them uncompressed, then people can view them in their browser. PDFs are already reasonably well compressed. I always put the file size of PDFs by the link to warn dial-up users.
A good program to produce them is Serif Page Plus. A free PDF printer driver like Primo PDF is useful for producing them from any Windows application.