Berlin Tegel comes to mind from the description in the OP, which is indeed living on borrowed time. Each gate has its own check-in desks, individual security channel, immigration desk for arrivals and seating area for departures.
Amsterdam and Prague are two examples of large airports in Europe, where non-Schengen departures involve security screening at the gates. This is mainly to make non-Schengen transfers as easy as possible (i.e. passengers can enter the terminal and proceed directly to the nest gate, rather than being sent to a centralised area).
Last edited by EuroWings; 1st August 2012 at 11:23.