In preparing the first mission for my players, I developed a fondness for a particular henchman (henchwoman?), and plan to use her as a recurring villain. Now, if your players are anything like mine, that's not an easy task: they tend to leave only bodies behind. And they can be very efficient at making sure no one escapes.
But, in this case, with the characters being "good guys," working for the CIA, and operating in a friendly country (Canada), there is incentive for them to accept surrenders.
So, when my henchman was cornered, surrounded by PCs, with little hope of escape, she tired something new (for me, as gamemaster): she surrendered. The team took her back to their headquarters, and turned her over to their superiors. Who, in turn, reported her capture to their superiors in Langley, who ordered her transported to a secret prison . . . elsewhere, for interrogation.
Which means, ultimately, that she was no longer under the direct control of the PCs. They got a report a few hours later that she had slipped out of her manacles, killed the two goons transporting her, and escaped, to vex them again later on, and there was nothing the PCs could do to prevent it.
(This is probably not a new idea to most GMs, but it was an epiphany for me.)
Next time, of course, the PCs will not accept a surrender, unless I can manipulate the circumstances such that there are many witnesses, especially local police (and I can).
What other tricks have you seen to keep that special NPC from becoming dog food?