The best way (in my opinion) is creating a custom theme and replace the logo() function.
class qa_html_theme extends qa_html_theme_base
{
function logo()
{
$this->output(
'<DIV CLASS="qa-logo">
<a href="/url/that/you/want"><img src="/images/yourlogo.png" /></a>
</DIV>'
);
}
}
If you prefer to change qa's core, the logo is generated in qa-include/qa-page.php line 610 (version 1.5), but remember that this file will be replaced if you update the software version..
$qa_content['logo']='<A HREF="'.qa_path_html('').'" CLASS="qa-logo-link" ...