Supposedly, the Rabbi (Judah Loew ben Bezalel) created a golem out of mud. When a Nazi officer went in to the attic (or Genizah, a storage place of old writings), the legend says the Golem came alive and killed him. Supposedly during the war the Gestapo didn’t enter the attic and the church was preserved. The attic isn’t open to the public, further preserving the mystery!
The Church of St James in Prague is famous for the legend of a theif who tried to steal the jewels of the Madonna inside. As the story tells it, the statue came alive and clamped down on his arm, and he was stuck there until the morning, and the only way to free him was to cut off his arm.
The story, however, doesn’t seem to be enough to warn off prospective theives. Hanging just near the door is, supposedly, the 400 year old mummified arm of the thief. So you look up and see this manky, leathery twig like thing that no longer even looks like an arm. It’s pretty sick. But the rest of the church is quite pretty once you get past that!