In January 1983, (AUDIO: The Burning Prince) Omega established his base in Amsterdam during his plan to bond with the Fifth Doctor using his biodata extract. He captured Colin Frazer, Robin Stuart and Tegan Jovanka. At this point in time, the city was located on the curve of the Arc of Infinity when Omega had shifted it: Amsterdam being below sea level helped to maintain pressure for fusion conversion.
The Doctor chased Omega through the city to a small dock. There he shot him with a matter converter to prevent him willing his destruction and causing the destruction of the world. (TV: Arc of Infinity)
In 1989, when the Czech government stopped blocking Radio Free Europe, Rhoda Hoffman heard about the Rembrandt Museum in Amsterdam. She told Amy Pond that maybe someday she could see it. (COMIC: The Broken Man)