Speaking of trolls doing naughty things in dark places...
Has anyone suggesting that certain creatures might be harmed/destroyed/turned to stone by sunlight?
Ok, probably someone has. But how about connecting it to cave adaption? Higher degrees of cave adaption might cause from light to serious burns, then immolation, and then finally a total atomic shift (petrification).
Creatures like Medusa might actually be able to use this as a weapon, causing normally immune or only lightly cave-adapting critters to have a violent allergic reaction to sunlight (explaining the whole "petrifying gaze" thing.), making such creatures more dangerous on the surface, during the day, than they would be, underground or at night.
Speaking of light, how about the use of mirrors to reflect it? That could be used to light our Fortresses (when lighting gets in), allowing for the pleasantly "dwarfy" combination of high-grade metalwork and strategic architecture.
It could possibly be used as a weapon against certain creatures (or not--maybe mirrored light isn't as potent as real sunlight, or potent at all.).
HFS might possibly use souls themselves, somehow, as a light source. These might work like sunlight, but on touch, giving the possibility of stealing them from the HFS for use as weapons.
There might also be some kind of "sunstone" gem underground, that would duplicate this touch-effect.
This could ofcourse be used both by, and against, our dwarfs.
Presence of this "gem" (or whatever) could explain why plants can currently grow underground, and could then be used to duplicate this feature-but much more rarely-in later versions of the game.
On the flipside, darkness itself/shadows themselvex might be a more complex thing, in a fantasy world that contains undead and HFS. Perhaps, deep underground, there might exist a "living darkness", which-while it may not do anything on it's own (then again, it might)-could allow strange effects to occur.
This might exist along the lines of the suggested "aquifer of living ooze" in the OP--as a resource, as a critter, as a spawner of critters, as something for the Magic Arc, etc.
It might even be used to reverse the petrification effect suggested in the beginning of this post, and could then perhaps be destroyed with the use of mirrored light (reverting back to normal darkness permantly, or simply growing back again, over time.).
Maybe there could be some type of gem that (like the sunstone generating sunlight), could generate this type of special darkness--and maybe be used to create pockets of permanent darkness that can *only* be reversed by actual sunlight--mirrored or otherwise.
Perhaps there could be fanciful plants/fungi that can only be grown in the "living darkness". Or it might cause other unnatural things to grow.