This topic basically exists for what it says it does. I'm trying to devise missions to be played in an environment that is inimical to your fighter, yourself, and/or your fighter's systems. I'll outline my own concepts below, but other ideas are welcome (and preferably a justification or several).
We already have subspace, which we know renders shields inoperative. We also have nebular (and presumably, atmospheric can make the same conditions) electrical storms with EMP effects.
One of my current concepts is a similar situation to subspace, but instead the conditions are dense nebular or atmospheric, and the amount of particulate matter means that you cannot activate shields or that they cannot be kept up.
I've also envisioned missions that will penalize you if your shields go down, either subsystems (nonshielded ones like comms and nav, not stuff you need to move or shoot; I'm not that cruel), or actual hull damage. Radiation, heat, whatever, mostly situations suited to being too close to a star.
Any other thoughts?