remove_action( 'wp_head', 'feed_links_extra', 3 ); // Display the links to the extra feeds such as category feeds
remove_action( 'wp_head', 'feed_links', 2 ); // Display the links to the general feeds: Post and Comment Feed
remove_action( 'wp_head', 'rsd_link' ); // Display the link to the Really Simple Discovery service endpoint, EditURI link
remove_action( 'wp_head', 'wlwmanifest_link' ); // Display the link to the Windows Live Writer manifest file.
remove_action( 'wp_head', 'index_rel_link' ); // index link
remove_action( 'wp_head', 'parent_post_rel_link', 10, 0 ); // prev link
remove_action( 'wp_head', 'start_post_rel_link', 10, 0 ); // start link
remove_action( 'wp_head', 'adjacent_posts_rel_link', 10, 0 ); // Display relational links for the posts adjacent to the current post.
remove_action( 'wp_head', 'wp_generator' ); // Display the XHTML generator that is generated on the wp_head hook, WP version

http://wpengineer.com/wordpress-header/

The following is just a list of actions you can remove. Just grab the ones you need.

Cleanup Wordpress Header

wordpress

PHP