I like David's response, since it gives me the flexibility I need. However: correct it to:

<ul>
{% for p in pages %}
    {% unless p.show_in_nav == false %}
    <li><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
    {% endunless %}
{% endfor %}
</ul>

(the only difference is prefixing p. before show_in_nav)