Per the microformats The microformats process this page documents common examples of HTML navigation mechanisms out of which we may want to construct a sitemap.xml.
There would be no difference here really between websites and webapps, both use HTML elements for nav in the same way.
As per any decent POSH citizen the BBC's website uses a simple list element for navigation. The BBC admirably use very standard attributes.
<ul id="blq-nav-main"> <li id="blq-nav-news"> <a href="http://www.bbc.co.uk/news/">News</a> </li> ... </ul>
Apple use the same construct.
<ul id="globalnav" role="navigation"> <li id="gn_store"> <a href="http://store.apple.com/uk"><span>Store</span></a> </li> ... </ul>
Subjectively not so semantic in terms of markup.
<div id="userpanel"> <a href="/extras">Extras</a> <span>.</span> ... </div>
Existing practices and patterns
While the semantic markup differs slightly between these different example mechanisms, and many others, a common theme is the use of the link element. We have always used the same for our own sites.