Use the German national rail company website for schedules anywhere in Europe: http://reiseauskunft… There are “overnight” trains — direct trains, scheduled with few stops and to give you 8 hours of sleep time — between most major cities that are more than about 5 hours apart on day-time high speed trains.

My rules of thumb to choose the method of transportation:

Travel time by train less than 5 hours: take a day train
Travel time 5 to 7 hours: look for a cheap flight. Choose train or flight based on whichever is cheaper
Travel time over 7 hours: fly (unless prohibitively expensive) or take an overnight train

Overnight trains can be exhausting. You sometimes don’t get much sleep and it’s disorienting to arrive in a new city at morning rush hour — when all you want is a nap and a shower and you can’t check into your hostel until late afternoon. Flights can also be very tiring with the hurry-up-and-wait of rushing to the airport, waiting in long check-in lines, security time, flight time, getting from the airport to city center. Therefore I limit the total of overnight trains and flights to an average of about 1 a week with no more than 2 in any 5 day period.

Overnight trains are more expensive than day trains as they always require reservations in addition to the ticket. Plan on reservations costing 4 to 12 euros for a seat (not available on all overnight trains), about 20 to 30 euros for a berth in a 6 berth couchette, 30 to 40 euros for a berth in a 4 berth T4, and on-up for more private and/or luxurious accommodations.