How do I modify the individual links on comments (reply, delete, any others I add in Flags, etc...)?
thanks to your link to the theme_links i managed to solve my problems, so here's how i would solve yours.

the idea is to split the links in two parts, one to print before and the other after the content.

$group = $content['links']['comment']['#links'];
$plain = array();

if( isset($group['comment-like']))
{
    $plain['comment-like'] = $group['comment-like'];
    unset($group['comment-like']);
}
if( isset($group['comment-reply']))
{
    $plain['comment-reply'] = $group['comment-reply'];
    unset($group['comment-reply']);
}

$first = $content['links'];
$first['links']['comment']['#links'] = $group;
$second = $content['links'];
$second['links']['comment']['#links'] = $plain;

//before the print render( $content);
//note: apparently, you can't add a class to the &lt;ul&gt; element from here, so you should manually wrap it and fix your css accordingly
print '&lt;wrapp class="something"&gt;'.render($first).'&lt;/wrapp&gt;';

//after
print render($second);