Is there any app that returns a list of cities in Europe for direct train travel by entering the departure city?

There is an exact web app that does this work - https://direkt.bahn.guru.

For example, here is the result of Krakow Glowny as the departure.

This app only allows you to search by the station, not by the city. So in order to get all the direct trains from one city, you must repeat the search with all the stations available in a city - in the case of Krakow, Krakow Glowny, Krakow Zablocie and Krakow Plaszou.

Deutsche Bahn's website has a Arrival / Departure lookup page, which will show you where all the trains departing from a particular station go to - including intermediate stops as well as final destinations. It works quite well for most of Europe, though it seems to only give you results for 1 hour of departures at a time.

You can check following train websites, you only need to enter your departure city and your arrival city, it take care to search for you all transport connections available (train, bus, ferry, walk)

• ÖBB www.oebb.at/en, Austria, (Better UI/UX but does not consider ferry connections)
• SBB www.sbb.ch/en, Switzerland
• [DB] www.bahn.com/en , Germany

For most of the journeys you can buy everything in a single ticket that includes all the connections, and if not, get a detailed trip plan.

I recommend also their mobile apps, their are really accurate, show you the preview journey and up to date with possible delays.

Enjoy traveling!

Many booking sites allow you to select an origin, and then the destination menu is auto-filtered to what's available. (Although on some sites, that includes transfers that can be put on the same ticket.)