There is a Euronight 499 train from Munich to Zagreb, departing at 23:50 daily. What is the price for that journey (one-way, cheap seats) and how can I book it online?
ÖBB (Austrian Railways) will sell you a ticket on EN 499 on their website. As of this writing it costs €39 for a seat (advanced purchase price), including free reservation.
Add €20 for couchette, which includes a "small breakfast". Or, add €35 if you would like a sleeping cabin including the same breakfast and access to "washing facilities".
I do not believe it is possible to book this online. When I traveled this route I checked every possible railroad booking site in Europe and it was not possible. I ended up purchasing this ticket one hour prior to departure at the international window in the Zagreb train station for the Croatian kuna equivalent of €59 for a bed in a 6-berth sleeper couchette.