<body id="doc[[*id]]" class="sect[[UltimateParent]]">
<li class="goto[[+wf.docid]] [[+wf.classnames]]"><a href="[[+wf.link]]" title="[[+wf.title]]">[[+wf.linktext]]</a></li>
#doc1, .goto1 { background: red; }
.sect2, .goto2 { background: blue; }

I target resources by adding classes and/or IDs to the body of the every resource.
Then you could also add the ID of the target resource to the class of the Wayfinder item templates, to style nav items per resource.
<li class="goto[[+wf.docid]] [[+wf.classnames]]"><a href="[[+wf.link]]" title="[[+wf.title]]">[[+wf.linktext]]</a></li>
This way you can target styles at individual pages or pages in a particular container. Then the CSS:
#doc1, .goto1 { background: red; } .sect2, .goto2 { background: blue; }