To change top level admin menu items order you’ll need two hooks, two filters, and one function. Put the following code in your current theme’s functions.php:

function wpse_custom_menu_order( $menu_ord ) {
    if ( !$menu_ord ) return true;

    return array(
        'index.php', // Dashboard
        'separator1', // First separator
        'edit.php', // Posts
        'upload.php', // Media
        'link-manager.php', // Links
        'edit-comments.php', // Comments
        'edit.php?post_type=page', // Pages
        'separator2', // Second separator
        'themes.php', // Appearance
        'plugins.php', // Plugins
        'users.php', // Users
        'tools.php', // Tools
        'options-general.php', // Settings
        'separator-last', // Last separator
    );
}
add_filter( 'custom_menu_order', 'wpse_custom_menu_order', 10, 1 );
add_filter( 'menu_order', 'wpse_custom_menu_order', 10, 1 );