add a simple counter and conditional check:
$pages = get_pages('child_of=10');
$counter = 1;
if ($pages) {
echo '<ul class="projectthumbs">';
foreach ($pages as $page) {
if ($counter == 3){
$class=" class="YOUR_CLASS"";
$counter = 1
}else{
$class="";
$counter = $counter +1;
}
echo '<li'.$class.'><a href="'.get_permalink($page->ID).'">';
echo get_the_post_thumbnail($page->ID);
echo '<span class="projectthumbtitle">';
echo get_the_title($page->ID);
echo '</span>';
echo '</a></li>';
}
echo '</ul>';
}