My self-made ePub file passes the validity checker, but the table of contents doesn't work when I open it in Stanza iPhone.

Does your TOC look like this?

<item id="ncx" href="toc.ncx" media-type="text/xml"/>

If so, the "media-type" is incorrect. It should read:

<item id="ncx" href="toc.ncx" media-type="application/x-dtbncx+xml"/>

The fact that epubcheck doesn't validate this requirement in the spec is a bug in epubcheck itself:

http://code.google.com/p/epubcheck/issues/detail?id=21

Comments

There are lots of doubts are

There are lots of doubts are aroused in the frequently asked column. Some of the doubts are their chapter listening will not have any sense. They all want Lexcycle support. All know that there are problems with stanza desktop or iPod in file sharing. Some of them upgrade their stanza iPod then all their books are getting disappeared. Some of them cannot restore their books. Their iPods become unstable after installing stanza that means unwanted lockups occur. Rapid Prototyping