You can now send emails via the Pardot API! One-to-One and List Emails can be programmatically sent with all the benefits of our regular email tracking and reporting. This is really great for clients who want to do specialized integrations with us to send and track emails of all kinds (account activations, status updates, and other very personalized emails). You can send dynamically generated content (e.g. that a third party system pushes up to Pardot on send) or you can use an existing email template you have created in Pardot.
Future enhancement (soon): The next step would be allowing clients to send operational emails (emails bypassing opt-outs and not needing an unsubscribe address) such as billing notifications and other mission critical items.
November 6, 2013 Update: Woohoo — you can also now send operational emails (not requiring opt-out language and bypassing marketing opt-outs) such as billing reminders, system notifications, and other non-marketing emails to clients by adding a parameter in your API call. Note that you must have access to operational emails to be able to do this (your client advocate can turn this on for you if you have a stellar sending reputation and a valid business case).