The Body Horror segments of the new Battlestar Galactica Reimagined movie Razor are not as disturbing as the Hybrid, especially compared to the Minority Report hybrids already seen: an old man, responsible for the aforementioned Body Horror, talking cryptically and accurately about events still to come, about a main character being the root of everyone's doom, all while sitting in a tub of goo with cables going in and out, and finally reminding us, "All of this has happened before, all this will happen again. Again. Again. Again. Again," before calmly dying.
The first episode, '33', where the Cylons relentlessly appear and attack every 33 minutes - pure 200 proof nightmare fuel.
The Cylon attack on the colonies in the original miniseries bothered me to no end. I think it might have been the orbital view of the mushroom clouds silently bursting over the whole planet, knowing that everyone you knew who wasn't right there with you is now dead. Similarly, the scene where the vipers go dead during a cylon attack and the pilots are trapped in hunks of metal, dead in space, helpless, waiting to be killed.
The depiction of what was going on planetside in the feature length episode The Plan was pretty grim too. Highlights include a montage of various Colonies (some of which we had never seen before) being depicted as burning ruins, Tory and Ellen Tigh being hit by the blast wave, the Centurions roaming the streets killing survivors and, for extra nightmare fuel, charred corpses of those too close to the blasts. The whole holocaust in general qualifies as HONF, and plays upon the (quite rational) fear of nuclear war.
The Pegasus approach to interrogating Cylons, be it the tortured, raped and Driven to Suicide Number Six Gina, or especially the scene in which officers from the Pegasus attempt to rape an unsuspecting and pregnant Sharon Agathon in a scene I can't watch without feeling physically ill. * shudders*
The Centurions boarding Galactica in "Valley of Darkness", particularly the very first time the characters run into one. Flyboy, Kat and Apollo are walking merrily through a darkened corridor, unaware of any problems beside the loss of power, when suddenly Kat screams, and Flyboy runs right into a seven foot steel monster. The thing flexes its hand briefly before tearing through Flyboy's chest with its metal claws (spraying Apollo with blood in the process), and then swatting him aside before he can even finish bleeding to death.
In the finale, the look on Tyrol's face when he finds out what happened to Cally. He's thoughtful, working through it, then you see his nostrils flare and he just goes O_o and promptly breaks Tory's neck. Remember, this is one of the nicest, friendliest characters in the series.
New Caprica. ALL OF IT! Although the end of the arc has heavy doses of awesomeness.