RUN AWAY!

I think GMs have a natural impulse to keep encounters going until one side drops (I know that is how I used to run encounters). This is one reason why some games have morale. Whether or not your game has this sort of mechanic, it is worth trying to see things from the point of view of your monsters and NPCs when they are getting trounced by the party. Most people don't want to die, and most animals or monsters have enough sense to back down when survival is on the line. This can also lead to interesting opportunities for campaign or adventure developments. Some NPCs might simply try to run away when they're bested, but others may take a different path to preserving their skin. 

Bargaining

One thing I've discovered is a lot of parties are not immediately willing to just let the bad guy off the hook because he suddenly threw his arms up in the air. They might not kill him (though that is absolutely an option for most groups) but at the very least they are going to take him prisoner or knock him out. A clever NPC might try to bargain with the party. He may even lie and send them on a wild goose chase to save himself. Overused, this loses its effect, but most parties will at least pause if they hear "Wait, I know a way to save your friend". 

The Traitor

Sometimes the party is fighting a group of opponents who are not all equally loyal to the big bad. When things get dicey, one of them might be willing to negotiate. If this is the case, and any others in the group are unwilling to betray their leader, this can lead to a fun scenario where alliances shift in the middle of a tense combat. If the traitor needs a little help from the party to maintain appearances with the higher ups in order to be of use to them, things can get interesting and complicated very quickly. 

New Found Respect

Sometimes beating a person in a fight earns you their respect. In extreme cases, the enemy's number two might have a change of heart and join the party. This is one you don't want to overplay and it ought to feel natural when it occurs. In one of my own campaigns, the party was being chased by an assassin who struck at them from a rooftop near their inn room. They ended up defeating her and discovered that failure essentially meant death from her master. So they showed her mercy and promised to help her survive. Not only did this gain her trust, she became one of the PC's disciples. 

Suicide

Some people don't fear death, and don't want to give their enemies the pleasure of killing them. This can be true in cases where grudges are being fulfilled. A NPC who wants to lessen the sweetness of his enemies revenge, may just kill himself when he knows its over. 

I'm Really on Your Side

This is a little like bargaining but a lot more interesting. It requires the NPC lie to the party, trying to earn their sympathy. Maybe he says he was forced into fighting them because the emperor kidnapped his sister, or perhaps he claims a misunderstanding ("They told me you killed my sister"). What makes this interesting is the players really don't know if it is true or not. In this case it isn't, the NPC is just lying, but sometimes they are telling the truth. 

No, I am Really am on You Side

Not every opponent needs to be in it because they are bad. Sometimes they get roped into doing bad things by others. Maybe the Emperor really did kidnap the guy's sister. As with the above, what makes his interesting is the party really doesn't know if he is telling the truth or not. 

The Bluff

Player Characters do this all the time, but it is easy to forget that NPCs can do it as well. Whether it is claiming they packed the mountain side with gunpowder and can blow everyone up with a simple gesture, or that they have the place surrounded, bluffs can give the players pause and force them to make a hard choice. This is especially true if the NPC claims something they were not expecting but rings true (i.e. "Too bad your bother bumped into my men on his way to town this morning, I'd hate to think what they will do to him if I don't return within the hour").