Watching Rojan the Kelvin crush the distilled solid form of one of the two Enterprise crewmembers in "By Any Other Name." Just knowing that one of those young innocent people had just died in such a cold display of power was sad enough, but (unless your paying uber attention I suppose) you don't really know which one. It sort of forces your mind to play those "lesser-of-two-evil" mind games where you feel guilty hoping for one or the other to survive. It wasn't gross, but more mentally disturbing.
Jedda getting zapped so unexpectedly in TWOK, and the TMP transporter malfunction are probably my top two for shock value.