Snippet to automatically assign a invoice number to an order when payment is successfully completed http://www.woothemes.com/products/print-invoices-packing-lists/

functions.php

<?php

// Add the following to the bottom of your theme's functions.php

add_action( 'woocommerce_payment_complete', 'set_pip_invoice_number' );

function set_pip_invoice_number( $order_id ) {
	$order = new WC_Order( $order_id );
	if ( in_array( $order->status, array( 'processing', 'completed' ) ) && function_exists( 'woocommerce_pip_invoice_number' ) ) {
		woocommerce_pip_invoice_number( $order_id );
	}
}