Most skills that go unused are neglected because some other skill does their job better.
Poison Dart runes: Kite builds were once popular because it was pretty much necessary to stay alive in Inferno. Now, with lower monster damage and better equipped players, kiting is usually a waste of time. And even if we wanted to kite, Numbing Dart isn't the best skill for it. Grasp of the Dead is a much better ranged snare. If we want a mana regen primary, Widowmakers is generally superior to Spinded Dart. If we want to rune Poison Dart for increased DPS, Splinters is better than Flaming Dart. Snake to the Face is an unreliable chance to stun a single target. That's simply not valuable in a game like Diablo 3.
Corpse Spiders runes: Spider Queen is somewhat useful when combined with Vision Quest since it provides low-maintenance uptime on the mana regen buff. Medusa Spiders is another kiting skill, which is unpopular gameplay type and doesn't work as well as Grasp of the Dead anyway. Blazing Spiders is another pretty useful skill. It does fairly high single target damage and has an extremely low mana cost.
Plague of Toads runes: This skill is difficult to use and produces mediocre results even under optimal conditions. It's just not efficient. Rain of Toads is the only really useful rune for this skill because it completely changes the targeting mechanics. Blizzard would have to boost the damage up to the level of most secondary skills to get players to seriously try using this.
Firebomb runes: all the firebomb runes basically do the same thing: AoE damage for low cost. If you're farming low MP with good gear, you can kill most things in 1 or 2 hits anyway, so coverage becomes more important than damage. Ghost Bomb has the best coverage of the Fire Bomb runes, so if you're going to use Fire Bomb at all you may as well use Ghost Bomb because it best accentuates what you want Fire Bomb to do.
Grasp of the Dead runes: the main use of Grasp of the Dead is for kiting, which is less popular now than it used to be. If you're using it to kite, you want to rune it for either increased snare or increased damage. The other runes are irrelevant because you wouldn't use the skill at all for anything else.
Firebats runes: Firebats is basically a cheaper but less powerful version of Zombie Charger. If you want to use a short-range AoE skill you're generally better off going for the amount of mana regen you need to use Zombie Charger (by which I mean Zombie Bears, of course) instead. Plague Bats is a pretty decent skill, though.
Haunt runes: Haunt is a single target skill that deals damage over time in a game that's all about killing whole packs of monsters as fast as possible. It's just an inherently bad skill for a game like D3 and will never be popular for general play. This skill will just never be seen much outside of uber bosses and PvP.
Locust Swarm runes: Locust Swarm is just like Ghost Bomb. It has excellent coverage but poor damage. It's great for low MP farming where you kill most things in one hit anyway so your main concern is just hitting them fast. I have no idea why you listed all five runes as largely unused because I thought a lot of people used Pestilence for low MP farming. (And it they don't, they should. It's a very good skill for that.) Devouring Swarm is a pretty good mana regen skill for higher MP's, too. The other 3 runes aren't used because they're just worse versions of Pestilence.
Zombie Dogs runes: The game classifies Zombie Dogs as a defensive skill and that's what most players use it for. Leaching Beasts and Life Link are defensive skills that help keep you alive. Rabid Dogs and Burning Dogs just add negligible amounts of damage to a skill that you don't slot for damage purposes anyway. Final Gift does have some use for players who use cooldown reductions to spam Zombie Dogs for Sacrifice builds, though.
Horrify runes: Horrify is not widely used at all because it's not a very good defensive skill. It scatters enemies around, making them less convenient to AoE and the cooldown is too long to really protect you from something dangerous. If you're going to use it as an actual defensive skill, Frightening Aspect gives the most reliable boost. The only other use for the skill is as a mobility booster, which is why Stalker is used.
Spirit Walk damage runes: Spirit Walk is our primary defensive skill and is slotted for that purpose. We don't want to be consuming an important defensive cooldown just to deal a minor amount of damage when we have so many other skills that are much better for that purpose.
Hex runes: Hex, like Haunt, is just not a skill that is well suited for this type of game. It's a single-target crowd control skill that we can't even aim in a game where we are almost always fighting multiple targets at once. The only real use for the skill is against champion packs in high MP, and even then it's not very impressive. This skill will never be popular without major changes.
Soul Harvest runes: Most people don't use Languish because it's just another kiting tool we don't really need and Grasp of the Dead is better for that anyway. We have much better mana regen tools than Swallow Your Soul too, especially because we usually want to use Soul Harvest at the beginning of a fight, when we tend to be full on mana anyway. Also, Vengeful Spirit is just so powerful for general play that it overshadows all other rune options for this skill.
Mass Confusion runes: Mass Confusion is not used because it has too long a cooldown, we don't need crowd control skills for the kind of low MP farming that most of us spend our time doing and it's not very reliable anyway. We just have better options.
Zombie Charger runes: Zombie Bears is so much more powerful than every other Zombie Charger runes it's not even funny. I have no idea what Blizzard was thinking when they set the numbers for this skill.
Spirit Barrage runes: Spirit Barrage is a somewhat slow projectile that only modestly outdamages primary skills like Poison Dart and Corpse Spiders. It's got some uses, especially for piercing walls, but it's just a mediocre skill and won't ever be very popular unless Blizzard buffs the damage again. That's why the only popular rune is Well of Souls.
Acid Cloud runes: like Locust Swarm and Fire Bomb, Acid Cloud is used to get good coverage for rapidly AoE'ing packs of monsters in low MP situations. That means the increased area rune is inherently the most useful for supporting that playstyle. Kiss of Death and Corpse Bomb significantly alter the mechanics of the skill, but not in a way that actually supports its primary role. Lob Blob Bomb is good for tanking higher MPs, though.
Wall of Zombies runes: Wall of Zombies is not used much because it's a kiting skill and that playstyle isn't popular/necessary anymore, and the cooldown has always been too long to boot.
Gargantuan Wrathful Protector: Just read the tooltip. It looks terrible. This is another of those, "How did they think this would be useful with those numbers?" kind of skills. The Big Stinker rune gives some nice sustained damage even when the thing is wandering around without swinging, though, and works just fine.
Big Bad Voodoo runes: This is another skill with a cooldown that's really too long for what it does. Also the fundamental design on the three unused runes just sucks. It's already hard to stay in the radius for the full duration so the increased duration rune is unappealing. The cooldown makes it a terrible way to generate Zombie Dogs (whether you're using Sacrifice or not) so Boogie Man is unappealing. Ghost Trance is a bad way to try and heal yourself because it forces you to stay in the radius.
Fetish Army: this skill is not used because its cooldown is way too long for the effect it has.
Edited by Vaidency#1113 on 2/12/2013 11:36 AM PST