Also note that the evil responses are HILARIOUS. "I've told you before, citizens are a RENEWABLE resource" for one of the ones where you have to sacrifice people. Most of the others require too much context to describe here.
In the larger picture, it's generally better to be seen as a Good civ than an Evil one, since other civs will be automatically distrustful of you if you're Evil, and more trusting if you are Good. Being Evil and attacking everyone around you will also quickly lead to other civilizations ganging up on you. It is possible to play the game this way, but you had better make sure your military and economy can handle that much conflict!
In Master of Orion 2, after conquering a planet in a ground offensive, you have the option of committing slow genocide after looting all the new tech and then moving in your own race. For the impatient, a modest fleet can destroy up to 30 million inhabitants in one round of epic bombing or even blast the planet into asteroids. For the impatient and greedy, biological weapons can wipe out the populace instantly while leaving the tech intact... but the rest of the galaxy will hate you for it.
A race that chose Democracy as its government cannot eliminate conquered colonists. It can, however, still use biological weapons or conventional bombardment.
Sid Meier really seems to like this trope.
In the original Civilization, there were two ways to win. You could open a whole new vista for the human race by leading the colonization of Alpha Centauri, in a triumph of learning, technology, and the indomitable human spirit. Or you could just conquer the world by force. Now guess which was not only easier, but gave you more points.
Sid Meiers Alpha Centauri allows you to be a genocidal maniac. You can order your units to obliterate cities you've just conquered, killing every man, woman, and child inside in the process; the game gives you the approximate number of people you've murdered each time you do this. You can even annihilate YOUR OWN cities in the same way. You have a thing for nukes? How about Planet Busters that can engulf the heart of your enemies' civilizations in nuclear flame, instantly erasing three or four bases and leaving an inland sea where their capital city used to be? Use enough of these and you may melt the polar caps, drowning everyone on the planet who happens to live near a coastline. Maybe you want to commit mass murder without the pesky ecological side effects of nuclear holocaust? Just depopulate entire continents with nerve gas, or have your units destroy every farm in an enemies' territory and watch their population drop as their bases starve to death. If you prefer biological weapons, you can breed Mind Worms to paralyze your rivals with horrific hallucinations while they implant ravenous larvae into the still-living brains of their victims. The list goes on. And the icing on the cake? You can do all this as the leader of a free-market democracy under the aegis of the United Nations!
Sid Meier's Colonization, however, really took the cake. The manual that came with the game talked specifically, and in no uncertain terms, about how evil the treatment of the American Indians by the European colonists was. The game itself, however, heavily rewarded the destruction of the Indians. About the dozenth time they have launched an unprovoked attack on one of your colonies, you will likely feel tempted to adopt a particularly violent form of Manifest Destiny.
Beyond even that, the Aztec and Inca peoples are deliberately set up to be the game's Money Spiders: Sacking their settlements is guaranteed to always yield a full galleon load's worth of treasure.
Step one: Complete the Hub plot in X3: Terran Conflict. Step two: Use your newfound control over the game's Portal Network to connect four Xenon sectors to a populated area. Step three: Laugh maniacally.
If another pilot ejects from his ship (whether because you bought it from him, or because he offered his damaged ship in exchange for you not finishing him off), they'll start floating towards the nearest space station in their spacesuits. You have the choice of leaving them alone, using them for target practice, or scooping them into your cargo bay and enslaving them at pirate bases.
Age of Wonders and its sequel Age Of Wonders 2 The Wizards Throne encouraged this. Poison Clouds on a city? Check. Blowing up the forge to deal damage and set back construction? Done. Steal your enemy's supply of mana, and use nearby mana pools as places to launch magical attacks from? Done and done. Not to mention the evil races had plenty of abilities designed to kick opponent's teeth in (Charm is a very awesome one-make the enemy's big, badass Behemoth kill the entire back line of archers!)