How did I enable atom feeds in a fresh WP3 install?

You can use the wp_meta hook:

function extend_meta() {
    echo '<li><a href="' . get_bloginfo('atom_url') . '" title="' . esc_attr( __( 'Syndicate this site using Atom' ) ) . '">' . __('Entries Atom Feed') . '</a></li>';
}

add_action( 'wp_meta', 'extend_meta' );