If I had ghosts in a campaign, I'd run the first encounter having the PCs be practically incapable of harming them. They'd have to learn what actually harms ghosts -- in Supernatural, it's salt; in my game, it might be weapons etched with prayers, or spells cast with blessed implements -- track some down as a mini-adventure, and then go save the day.
(And even then, these weapons still only deal half damage to the insubstantial spooks.)
For extra fun, mix things up every once in a while. Why would the ghost of an orc warlord obey the same metaphysical rules as the ghost of a human noble? Maybe orcs think that blood is sacred, so you can only hurt a ghost if your weapon is covered in blood (or if you're bloodied). Maybe ghost dragons can only be harmed by weapons either stolen from their hoard, or crafted from items once in their hoard. Perhaps a Dark Sun defiler wraith can be harmed if you're holding an unplanted seed in your mouth.