There's a handful of traps that stick in my mind, like the rack in Saw III or the blood sacrifice in Saw V. Those are disturbing, but I mean... it's horror, isn't it? Granted, I don't get affected by gore directly that much, but there's still a level of horror to how much the human body can endure.
I still prefer Alien, Evil Dead, Halloween and Nightmare on Elm Street as horror franchises, but Saw is still pretty damn good in my opinion. Gore is sometimes necessary to invoke a negative reaction. It's the tension, desperation and "horror" that comes from such contraptions.
Alien is my favourite horror franchise by far, and the Xenomorph's life cycle is very disturbing. Of course, I don't just like it because of the Xenomorph, but rather the world, the environment, the corporate undertones, the sets, and the characters... but without such a deadly adversary, the series wouldn't have that same feeling of hopelessness. Horror leaving an impact on you after you've seen it is because it did its job well.
These are just my own opinions, by the way.