The first episode, '33', where the Cylons relentlessly appear and attack every 33 minutes - pure 200 proof nightmare fuel.
Gaius having a nightmarish vision of Adama drowning his metaphorical daughter.
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 look of absolute cold fury on Adama's face when Starbuck confesses her role in Zak's death. Katee Sackhoff has said you're not seeing acting from her in that scene; she was genuinely terrified that he was about to beat her up.
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.
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*
New Caprica. ALL OF IT! Although the end of the arc has heavy doses of awesomeness.
During some of the parts with Kara, if you listen very carefully to seconds without music or dialogue, you can hear people screaming.
The Body Horror segments of the new Battlestar Galactica 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.
From the Razor Flashbacks, the destruction of Columbia, specifically the screaming of her crew over the radio after the ship has already exploded, until it finally cuts out.
Leoben Conoy snapping his chains and turning over a steel table like it was nothing before attacking Starbuck. If You look closely, there's a brief moment after he breaks his cuffs that the battle-hardened Starbuck, who has been laughing at him the whole time, jumps back and starts looking genuinely terrified.
Dualla's sudden, shocking and violent suicide after pretending to be happy will leave a mark on even the most well-adjusted.
In season 4.0, even though she was The Scrappy, Cally's death by airlock (in front of her son no less) is absolutely chilling. Even worse, before Tory showed up, there was every indication that Cally planned to throw herself out the airlock, along with the aforementioned infant son. Let's repeat: a baby, being subjected to all the horrible things empty space does to you before killing you. Thankfully, the writers didn't take it that far; just dangling the possibility was horrifying enough.