When I have my iPhone 4s on vibrate only mode (side switch down), sometimes I a single vib alert from an unidentified app. None of my apps have applicationIconBadgeNumber set, so, what the heck is making it vibrate?
Look in Settings > Notifications for an app that only shows "Sounds". If you have more than one app, turn on Badges or Banners (temporarily) until you get the next notification. The app with the new badge should be the culprit.
Otherwise, go through the list one by one and disallow Sounds for each app successively until you find the offending app.