I can't say that this is the best solution, but...
I found a quick way to make nice looking and portable changes to the navigation 'portlet' in monobook was to make changes to:
/lib/tpl/monobook/main.php
Look around this tag:
<div id="p-x-navigation" class="portlet">
and add things like:
<li> <A HREF=".">Start</A><br>
<li> <A HREF="./doku.php?do=index">Index</A><br>
<li> <A HREF="./doku.php?id=<?php echo $ID ?>&do=index">Namespace index</A><br>
<li> <A HREF="./doku.php?do=recent">Recent Changes</A><br>
Conceivably you won't be making many changes to the navigation portlet, so modifying this code isn't a big deal. Additionally, it's not tied to a certain url, and seems (to me) to be very portable.
Here's a quick example of a non-business wiki (that I'm working with at the moment) which is using a pretty modified version of monobook. None of this links in the picture are tied to a particular url (this wiki is kept on a portable drive).