VoodooPad supports a couple of cool AppleScript commands that might be useful to you. Besides the usual document based commands that go along with standard Macintosh applications, VoodooPad can also be told to export documents as HTML, RTFD, or text.

Here's a simple example for exporting as HTML:

tell application "VoodooPad"
  export document 1 as HTML to "/Users/jimi/Desktop/mywebsite"
end tell

You can also substitute the HTML keyword for "RTFD" or "text" like so:

tell application "VoodooPad"
  export document 1 as text to "/Users/jimi/Desktop/mystuff"
end tell