All the enemies are dead except the boss who says he surrenders, what do you do?

[Lord Vukodlak]

In one campaign I was in our group of adventures rarely fought people during our quests.(by people we any humans or Demi-humans) it was almost always monsters. When we did face people not only did we accept surrender we made every effort to bring them in alive.

This included a serial killer who made a suit from the skin of his victims. The murderer was tried and executed. The only time lethal force was used against people were against those of which there was a defacto state of war with. And if someone surrendered we either took them as POWs or let them go so long as they left their weapons behind.

But even as a general rule, do you execute a surrendering big bad? Well usually those types of people have done stuff that will earn them and execution anyway if you did bring them back for trial.
So why are they even surrendering?
In 3rd edition paladins are lawful good divinely empowered instruments of justice. If they can not be brought back for trial and their sentience carried out safely. Then it may be the paladins duty to carry out that sentience on the spot.

“Lord Darkhold, you murdered scores of innocent men, women and children without care or remorse. Turned them into your armies of the dead and unleashed them upon your enemies. Any prisoners you took were worked to death in your iron mines. For your crimes against sapience the sentience is death!”

And if the big bad didn’t do something worthy of a death sentience. You might have to question why you slaughtered all his men.