What type of ancient siege weapon is referred to as a stone-throwing engine?

The term "stone-throwing engine" refers specifically to the design and function of a siege weapon known as a catapult, which was used extensively in ancient warfare to hurl projectiles at enemy fortifications. The catapult is characterized by its ability to launch large stones over substantial distances, making it an effective tool for attacking walled cities and fortresses.

The other options represent different types of ancient siege weapons. The ballista is primarily a large crossbow-like device used to launch bolts or heavy projectiles, typically not stones. The trebuchet is a more advanced siege engine that uses a counterweight to fling objects, which can include stones, but it is not traditionally referred to as a stone-throwing engine in the same sense as a catapult. The onager is another type of catapult that uses torsion to launch stones, but like the trebuchet, it does not share the broader definition of a stone-throwing engine as accurately as the catapult does.

Thus, the descriptions and historical context lead to the conclusion that the catapult is indeed the "stone-throwing engine" referred to in the question.