db_query and db_select
Since you are querying some tables to get the value of an entity field, I would rather use the EntityFieldQuery class.

To answer your question, what you want to achieve can be obtained by concatenating strings to the the query string.

$query = "The first part of the query";
$args = array();

if (isset($form_state['storage']['etat_livre'])) {
  $query .= "WHERE field_etat_du_livre_value = :field_etat_du_livre_value";
  $args[':field_etat_du_livre_value'] = $form_state['storage']['etat_livre'];
}

$query .= "ORDER BY field_etat_du_livre_value ASC, created DESC";

$result = db_query($query, $args);


As side note:


The query should not use back-ticks
The reserved words should be written in upper case