I'm asking primarily about cities on the continent in Europe that were (or were at risk of being) overrun.
As an add-on: Would they have been eaten in extreme cases (Leningrad) or even pressed into service?
Hi, hopefully you'll get some responses here, but meanwhile you may be interested in this one on the Berlin Zoo
There is a fascinating book by Diane Ackerman called The Zookeeper's Wife in which she tells the story of the Warsaw Zoo and the husband and wife team who ran it, during WWII. The husband had been good friends with the head of the Berlin Zoo before the war, and the Berlin zookeeper became a very high ranking Nazi, so he gave the Warsaw zookeeper some measure of protection. They did their best to keep the zoo going during the brutal Nazi occupation of Poland so they could use the tunnels in the zoo to hide and move Jewish refugees, without his benefactors knowledge, and right under the noses of the occupying force.
She also discusses the Nazi's animal eugenics program, in which they were trying to restore certain extinct species to the European forests, most notably the Aurora.
A really fascinating book that reads more like a novel than a history book. This is a prime example of my favorite WWII stories - those small heroes who fought against Nazi repression in any small way they could.