The passport will be stamped when you will pass immigration when entering Schengen area (Schengen port of Entry) and when you will exit Schengen area. Flights from one Schengen state to another are domestic flights, so there's no immigration control. There's no immigration control at frontiers of 2 Schengen states if travelling by car (but there may be unscheduled custom controls on the roads around the frontiers, this imply control of the travelling documents).
For Eurostar you have a commun immigration control at the last station before passing a frontier (I.E. French/English immigration in UK).
For ferries crossing the channel I don't know.