Well, there's the saving bonus, which I assume you know about. It's when you save all of the employees, and then you get something. Nothing much special, mind you, but you have a certain sense of accomplishment and all.

And then, there's the killing bonus. It's when you go around killing Mudokons instead of saving them. I don't know how many you have to kill exactly, but a good deal more than half. Keep track of that in the casualties column on the employee monitoring screens.
As for the bonuses themselves, I'm not intending to spoil it for you ;)
But I can't resist saying that the killing bonus in AO is really cool. Imo at least.

..damn.. I'll have to do that. I've never actually done that before o.O

Is it in all of the game?

It's in AO and AE both, supposedly, but in AE it never worked for me. It's in MO as well, but I can't give you any details since I don't have MO.

I don't think you can get the killing bonus on Munch's Oddysee without cheating. You need to save the fuzzles to get the spooce to get out of the door.

That is understood in the calculation of Black Quarma. It's the most killed whilst still allowing you to finish the game.