I learned to format epubs working from samples that I opened up in the Oxygen XML editor ... as well as from the Elizabeth Castro and Paul Salvette books.
Both Castro and Salvette say that the toc.ncx should start with the cover, title page, copyright page, etc. and then go on to the actual chapters. It is noted that if you are going to convert to mobi/Kindle formats that you need to remove the coverpage from the toc.ncx and renumber the play-list and all the toc-anchors.
The samples I have, from another developer, start with the table of contents and go on to the chapters. I have been formatting that way, but all of a sudden I am wondering if this is correct.
I do know that, as a reader, I do not want to have to page through the cover, etc. once I have started reading the book. I want to go back to the contents page. So there is something to be said for formatting the toc.ncx that way. (The frontmatter shows up fine if I make sure that it is listed properly in the content.opf.) It is also nice not to have to re-do the toc.ncx and toc-anchors when converting to mobi.
But on the gripping hand, sometimes the contents html page shows up in Calibre's and ADE's left-hand-side content displays, and sometimes I get a no-such-page error message. I see a heading, Table of Contents, then a contents page to which the link is broken. I have not been able to figure out what triggers the broken link problem. Fixed that; I cannot include a toc-anchor on the contents.html h1 heading. Removed it and everything is fine.