If you're running version 3.2 you should already have $postcount in index.php.
For the ad, put the code below into index.php, for instance before or after
PHP Code:
</div><!-- / Post -->
depending on whether you want to put it inside or outside the post container.
PHP Code:
<?php if ( (is_home() OR is_archive()) AND $postcount <= 1) { ?>
AD CODE
<?php } ?>
is_archive covers Category, Tag, Author and Date based multi post pages.
is_home covers the home page (if a static page is set as homepage then only the homepage of posts) including page 2, page 3 etc.