I found your post interesting because I hadn't heard of some of the modules you mention.
Of course, the best way for one machine to talk to another machine over the web is through some machine-sensible protocol: XML, soap, whatever.
That statement seems quite ambiguous to me. Are you talking about application protocols (e.g. HTTP, SMTP) or formats used in those protocols (HTML, RFC822)?
Either way, you may be interested in designing your systems RESTfully. I know I am.
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