Whew, 4+ hours to read this thread
It was worth it though, really interesting!
A couple of ideas I had for underground features, and the like:
First of all, on the subject of underground creatures, specifically antmen, how about giant termites/termitemen? They could live in vast towercap forests, and make war on antmen. Their soldiers would be naturally blind, fearless, and much more dangerous than the average antman. They wouldn't even be as (roundly) intelligent as antmen are, but they could be the consummate soldier/army race, utterly devoted to military endeavour, and intelligent enough to make use of found weapons/armour.
As far as a "race that's similar to, but the opposite of dwarfs" goes, that lives deep underground, how about a dwarf-like species (in appearance) that's really a form of sentient fungus? They'd start out the same size as dwarfs, but never stop growing, and they wouldn't die from natural causes, so the oldest members of the species would be powerful giants. The very oldest giants might even go dormant, and be used as living architecture by the younger non-dwarfs. These non-dwarfs would never go to the surface because sunlight would be deadly for them, and instead of getting drunk off of alchohol, maybe they could naturally (non-toxically) drink alchohol as a food/energy source, but instead of getting drunk, they'd recreatively consume powerful underground psychadelic 'shrooms to get high? And they might craft items like dwarfs currently do, but also grow items too, like elves, but from fungi. Unlike elves, they'd still eat meat, wage war, cut down trees, and do exploitive "dwarfish" things, but they'd be a lot more in tune with their-albeit weird-environment than dwarfs tend to be.
Immobile, but sentient, crystals would be fun too. You might eventually mine them, but they give you a fight! Maybe with some kind of energy weapons. Aside from not being able to move on their own, they might have vast intellects and powerful mental abilities, and you might befriend them, and educate them. Some dwarfs might even take to worshipping them. Being constantly exposed to them for long enough might increase the chance for other beings-dwarfs included-to go insane, or put the rare dwarf into a fey mood.
I'd really like to see enormous, blind catfish monsters--really vicious, carp-like critters that weren't the result of a bug, but actually existed as "killer fish" in the game, properly.
Aboleths might be good, too, D&D-based though they are. They're pretty distinctive and original, and make great villains to worry about. Maybe combine the "aboleth" idea with the above killer-catfish, to make something truly squamous?
On the subject of fossils: How about a (non-undead) fossil that's so enormous that a smallish fortress, or atleast several chambers, could be built inside of it? The beast (the father of dragons? an archaic whale? etc. ) it came from would be "from the dawn time", and not exist in the current game, but you'd be able to make out features like ribs, skull, spine etc. and maybe mine the teeth.
Also it would be great if there were small pockets of metals that we use today (aside from aluminum), like tungsten, etc. that could occasionally be found on the deepest layers.
Cave-pearls might make a nice gem-type that only appeared in the depths.
Localized magnetic and/or gravitic effects could also very well be encountered underground. Even some peculiar underground weather effects might happen. Suppose a certain cave occasionally "rained" sulfuric acid, or "snowed" tiny calcium crystals?