I'm pleased to say that you can now use @InvoiceId@
as a token in your notes or payment terms.
<img src="http://www.qr-code-generator.com/phpqrcode/getCode.php?cht=qr&chl=@InvoiceId@&chs=75x75&choe=UTF-8&chld=L|0"/>
If you place this at the bottom of your invoice terms, it should appear close to the bottom of the invoice:
After payment terms we have "Appended text" defined in Sales >> Invoice Customisation. We could potentially also achieve the same here, but then the barcode would then automatically appear on every invoice and estimate.