How would you manage to bring back some scary or disturbing feeling when using undead in your game of D&D?
I play a 3.X derivative, but the larger advice would also apply to 1e/OSRIC type games.
Regardless of the setting, I largely borrow gothic horror from Ravenloft. This is true mechanically, but also true because I'm coming at the game from the same direction. The fairy tales monsters, the things that go bump in the night - whether undead, lycanthropes, witches, monsters under the bed, evil fairies, or boogey men - are far more important to my game than the more usual D&D fantasy tropes.
So, for example, all undead have a supernatural aura of fear about them. With Ravenloft style Fear/Horror/Madness rules, this means that a ghost (for example) can literally scare the weak willed to death and drive the survivors insane. So even when the direct effects of undead are ignorable by the PCs, what they do to the surrounding 'innocent' population is horrific. The PC's may be fearsome slayers, but they are usually picking things up in the wake of the terrible mental and physical destruction evil has wrought.
Secondly, I treat necromancy as being very much like radioactivity. Sure, you can use undead as technology, and many societies have done exactly that, but even disregarding other ethical concerns (which are many), inappropriate and indiscriminate use of the technology leads to very bad things. Much like the radioactive plates of the 1940's where the plates had been painted with Uranium based paints because it produced a nice color, trivial use of necromancy typically has less than obvious but very terrible long term effects on the world. In many cases, this is mechanically represented in my games by representing the areas where necromancy has been misused as being desecrated, unhallowed, death aligned, evil aligned, and otherwise cursed. This renders undead that might otherwise be trivial into much more terrible foes, and makes the realms where undead are common a 'badland' greatly to be feared.
Thirdly, my undead typically have the legacy style powers of making you suck. While its true that PC's typically can invest in recovering from suck, there is still a level of fear/respect engendered here. The PC that treats undead lightly gets punished for it.
Lastly, engendering fear in the players is almost never a matter of mere mechanics, but depends on the presentation, immersion, and particulars of the player. Your mechanics might help push the game in that direction, but you are never going to get there with that alone.