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There is no recognized file suffix ".nav"
Under epub2, the toc.ncx is used for toc and pagelists (though few epub2 readers support pagelists in the ncx). Under epub2 landmark (semantics) are stored in the opf guide.
Under epub3 the nav is an xhtml document (typically named nav.xhtml or toc.xhtml) with a specified format. It stores the toc, landmarks, and pagelists.
Some people add a toc.ncx and opf guide info to their epub3 to allow them to be read on older epub2 only e-readers.
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