Standard mode means it will render using new W3 standards, quirks mode means it will render using the rules as they were before there was a standard.
This site has a pretty good explanation and links for more detail:
http://www.webmasterworld.com/forum21/7975.htm
Based on that, I would think that new content should be created in standard mode. I will keep researching to find out if there is any reason to use quirks mode, and why SharePoint Designer is defaulting to quirks. (Maybe because I’m using IE6 for previewing?)
Tags: CSS, IE6, quirks, SharePoint Designer, standard, style