I have trouble thinking of an effect nebulae could have on this type of game.
- Limiting travel speed (differently from normal) or preventing travel until appropriate tech is researched
- Preventing use of certain weapons / defenses / misc. ship parts
- Hiding fleets within them
- Damaging ships that spend time in them
- Nest for space monsters
- Being a source of a resource for players... eg. set up a Nebular Gas Refinery in a system inside the nebula, get supply of Verteron Particles
or Metaphasic Anti-Omega Radiation
used to unlock / speed production of a particular building / ship part
Yet, if it were of strategic importance, the current type of graphics are lousy indicators, since they fade out so gradually, it will be unreasonably hard to say if many planets are "in" or "out".
Then they'll have to be replaced. Maybe some volumetric fog could be generated instead.
Edit: If the nebulae were generated procedurally, then we could do some fancy stuff like lighting them, and having them cast shadows, by the star lights near them. Then if we were really bored, we could have nebulae generated and exapanding visible as the turns progress after supernovae, or new stars be created within existing nebulae... /Edit
Geoff: It sounds like what you want is a much more complicated, less homogeneous paralax view.
More complicated, yes. I'm not sure what you mean by "homogenous", though in a sense yes, as they're confined to the volume of the galaxy and react properly to zooming, rather than spreading out infinitely in all directions for no logical reason.
Really I'd prefer no cluttering and confusing background stars at all, as the map is much cleaner without them at all zoom levels, though if there have to be some, they might as well make some sense.