Fear, there is not near enough fear in D&D. And not the magic stuff I mean good old fashion I don't want to die" fear. I can't recall the last time any of my players ran away screaming. No matter how I set the mood or what I throw at them, except perhaps a big dragon, they'll at least try an fight it.
I don't play in a filthy world. In most of mine magic has improved living conditions to allow time for sanitation. Helpful druids and clerics fixing poor crops, wizards fixing water shortages, heck magic can improve a lot of things. Even simple cantrips can clean you up or fix ragged pants. Things like this work better in Eberron than say Darksun but even so it doesn't bother me too much to ignore it.
Food, weather and enviroment on the other hand always get my full attention in games. Timely fog, lightning or a rainstorm can add a lot to an encounter. Mud is slippery, wind makes balancing hard and fog shuts down archers and what not. I have ran several games where enviroment, weather, food, and survival are the main antagonists and they were great fun.
Ohhh I know something that is ignored... The food chain. I mean when you add up the biomass needed to support a breeding population of some of the larger creatures in D&D you'd have to conclude they eat rocks or magic or something. Thats an other thing that is often missed. Babys. Where are the young dire piglets. The baby displacer kittens. Ahh thats would be cute. Taking about taking a little wind out of your players sails. While searching the cave you find a bunch of, now motherless, displacer kittens. Well I guess I've gamed with people who would just sell them but I'm pretty sure I could make at least one of the girls in my current group cry with a situation like that.