What can you shoot with a ballista?

[Shin Okada]

Well, I don't know much about real ballista. But if I were a DM, I will not bother arguing with players what they can shoot and what they cannot. This is a fantasy game. If a 20-foot tall giant can throw a rock and shoot down a flying halfling wizard ....

 

[Ashtagon]

Even if that monster were doing flyby attacks, there is a considerable space in which it would be a significant horizontal distance from the ballista. I'd allow it to fire at any distance greater than, say, 30 feet, at an airbourne target doing flyby attacks. That's still inside range band one, so no range penalty.

 

[Jack Simth]

Rules for Ballista (and a few other things) are on page 100 of the 3.5 DMG.