I have two:
First one was a pilot in a Dragonstar campaign. A player created his 'we were a privateer ship for the Empire, until my brother sold us out' story, so I ran with it. The player started running a drunken pilot then, for reasons of his own, started sobering him up (never found out why. Great story hook though).His brother, on the other hand, started taking a drug that improved his flying while destroying his mind. As long as he did what the BBEG said, he got all he wanted. To the player, it was like looking into a twisted mirror.
That wasn't the clicher though. The party REALLY hated him after he infected the gnome's home planet with a virus that turns normal folks into anti-psionic ragers. The gnome just happened to be a psion. No was hurt, injured, or killed... so long as he never, EVER goes home again.
The second wasn't any one NPC per se. The campaign was running heavy espionage tactics, with doppelgangers as the BBEG's main spy network. I house ruled that target's of their Detect Thoughts ability didn't get a save unless they believed they had a reason for it (similar to disbelieveing an illusion). Nothing ticked the players off more than dealing with bad guys that knew their moves before they did. Completely threw off their sense of safety and control...