You can check your position within the loop using the current_post
var of the $wp_query
object, and insert markup at a specific spot or at some interval. A simple example:
while( have_posts() ):
the_post();
the_title();
the_excerpt();
// if current_post is 1, insert the div
// note that current_post starts at 0,
// so this will be after the second post's content
if( 1 == $wp_query->current_post ):
echo '<div>My div!</div>';
endif;
endwhile;