I have a request from my client who wants to sell customised software
on his website.
I was acknowledged that the ordering process should be in a way that
upon customer's transaction is processed, a download link to download the software will be made available.
He plans to use paypal.
You should look at the IPN option which will give you the most control over what is in the email. This can also be used to write to datbase or file on your web server.
You will need a script on your web server to process the IPN data
From what I remember you can use paypal's SOAP server to process payments (both paypal and credit card...but the latter requies a monthly fee). You'll get a response message back from the SOAP server and you can do whatever you want with it...like send an e-mail.