[Suicide Junkie]

I suggest creating a new "race" or two.

Their ships would be invulnerable, immobile little asteroid-like things, and you could place them in the areas you want your environmental effects to occur in. Preferably off the Z-plane so they don't get rammed.

They would just sit there, and throw lightning bolts at ships as they wander through the nebula, or invisible radiation beams from the surface of stars, and so on.

If you make a second environment race, you could make them enemies, and have them shoot effects at each other when there is nothing else around for them to attack.