Theres three routes in Europe that still use train ferries:

Puttgarden-Raedby between Germany and Denmark.
All Hamburg-Copenhagen EuroCitys use this route. The Train justs get driven
on to the deck and then driven off at the other end and shares the deck with
other cars and lorries, if you want you can get of the train and use the
facilities on the ferry or just wonder about the deck, its quite a novelty
seeing a train sat next to an HGV on a ferry deck.
See:http://www.railfaneurope.net/pix/dk/...-5092/P1010192
..jpg
&
http://www.railfaneurope.net/pix/dk/...92/dsb5285.jpg

Villa San Giovanni-Messina between Italy and Sicilia.
All through trains from the Italian mainland to Sicilia use this route, your
shunted in and out of the ship on to the rail deck and you have to remain on
the train for this one.
See: http://www.railfaneurope.net/pix/it/misc/ferry/pix.html

And finally from Trelleborg-Sassnitz between Sweden and Germany, used by the
nightly Berlin Night Express. Dont know much abut this one.