There are a few quests I've done so far that have really made me squirm. I play Horde, and you just know that most things the Forsaken are wrapped up in are going to be kind of dodgy. A lot of our early questing in Northrend concerns the Apothecary Society's attempts to find a Scourge-specific plague (...right), and that doesn't end particularly well. I can sort of accept that, because the quest series skates a thin moral line between plausible deniability on the character's part as to the apothecaries' true intentions, and what actually ends up happening. But there's one quest in particular that has nothing to do with the apothecaries that really gave me pause. It's actually one that has an Alliance equivalent as well, although it ends somewhat differently there.
If you're not that far into Dragonblight quests and don't want to be spoiled, I'm putting it behind the cut.