Add pagination to this following template

Firstly, you have 2 queries, the second is overriding the first:

<?php query_posts($query_string . '&pagename=&page_id='); ?>
<?php query_posts('posts_per_page=3'); ?>

Replace them with a single query:

<?php query_posts($query_string . '&pagename=&page_id=&posts_per_page=3'); ?>

Then modify your query as such:

'paged' => ( get_query_var('paged') ? get_query_var('paged') : 1 )

e.g.

<?php query_posts($query_string . '&pagename=&page_id=&posts_per_page=3&page=".( get_query_var("paged') ? get_query_var('paged') : 1 )); ?>