Here are some journey planners recommended by different contributors:

www.hourrail.voyage/en – practical advice and inspirational itineraries to help you organize low-carbon trips

rome2rio.com 

maps.google.com

For ferries: directferries.com     

For trains: The Deutsche Bahn (DB) app covers much more than Germany, you can actually use it to plan train journeys around many continental European countries.

Do you have other recommendations? Let us know!