"formerly known as 'cat arranger'" writes
I took two cats into a local shelter. One was a stray
and the other was a friend's cat....
They came home with a large chunk cut out of their ears. The
stray looks bad but the friends Siamese looking cat looks worse.
Is cutting a piece of their ears off the only way to mark ferals
and strays so they don't get operated on a second time?

You don't mention the locale in which this happened, but, if possible, ask
around at other shelters BEFORE bringing any more cats in.