I just noticed on the Bayern-Takt website that one of the privatized regional lines in Bavaria, Agilis, is now offering seat reservations on their trains (and these are regional trains). Agilis runs regional trains around Regensburg and from Ulm to Passau with lines to Landshut and Nürnberg. Reservations can be obtained at customer centers, from agents, and online, and are essentially free with a ticket, although there is a twenty cent charge from centers and agents, for personal service. Every one way ticket comes with one free reservation; there are 10 free reservations with a Länder ticket. If you already have a ticket (or rail pass), a reservation without a ticket is 1€. Reservations can only be obtained on the Agilis website; they are not available through the Bahn website. They even let you pick your seat reservation from a seating map, like for airline tickets. Unfortunately, the Agilis website is only in German.
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