I would add a property indicating the right positioning, and then use someting like the following code:

<ul class="left">
  <xsl:for-each select="umbraco.library:GetXmlNodeById($source)/* [@isDoc and string(rightPositioning) = '0']">
  <li>
    <a href="{umbraco.library:NiceUrl(@id)}">
      <xsl:value-of select="@nodeName"/>
    </a>
  </li>
  </xsl:for-each>
</ul>

<ul class="right">
  <xsl:for-each select="umbraco.library:GetXmlNodeById($source)/* [@isDoc and string(rightPositioning) = '1']">
  <li>
    <a href="{umbraco.library:NiceUrl(@id)}">
      <xsl:value-of select="@nodeName"/>
    </a>
  </li>
  </xsl:for-each>
</ul>

Hope it helps.