The season 2 finale, where Violet is lying half-dead in a pool of her own blood from a forced C-section by a woman who stole her baby. It's actually invoked in the next season, where Violet uses this experience as a Scare 'Em Straight moment to convince a pregnant woman to abort.
Amelia in season 5: Her ill friend asked her help in order to commit suicide (something which fails), then said friend nonetheless commits suicide later. Following this, she became an alcoholic, then a drug addict, her addicted boyfriend died of an overdose, she discovered that she was pregnant with his baby, and that said baby had no brain. She later gave her baby so that surgeons could harvest his organs for other babies in need of them. She managed to recover, but what she lived through was horrifying.
Everything about Sarah, the disappeared child in season 6, who was suspected to have been kidnapped (possibly by a pedophile). After many episodes and in-series 3 months, it turns out she was kidnapped by a pedophile, who, if he didn't abuse her, was clearly on the verge to finally do it (or simply kill her - what he meant to do was left ambiguous).
Worse still? We saw this pedophile beforehand in both the same episode where she was kidnapped and an episode prior where Sheldon winds up saving the man's life, even if Sheldon ponders if he should have soon after.
"Did you hear what happened to Charlotte King" (Season 4, episode 7). As much of a bitch as she is, it's still pretty hard not to feel bad for her when she is brutally raped by Nicholas Brendon.
Particularly disturbing is one scene where they have to stitch her wound without pain medicine. While she tries to "tough it out" she still loudly whimpers in agony as they do it.
Like the above, Sheldon had an encounter with the rapist.
