I've made a few changes to the template to create a default a threaded mode & would love for this to be an option in the admin section.

In /templates/default/subtemplates/index.tpl.inc:

Find this line and comment it out with <!-- and -->

<a href="index.php?mode=thread&amp;id={$data.$element.id}" title="{#open_whole_thread#}"><img src="templates/{$settings.template}/images/complete_thread.png" title="{#open_whole_thread#}" alt="[*]" width="11" height="11" /></a>

Find this line:

href="index.php?id={$data.$element.id}"

and replace it with this:

href="index.php?id={$data.$element.id}&mode=thread#p{$data.$element.id}"