Lets see....
Oblivion/Skyrim: taking and killing hostages until someone brings me the real Lusty Argonian Maid, becoming Listener of the Dark Brotherhood, killing and robbing anyone who looks anti-Imperial, crushing all those who stand in my path to personal power....
Rome Total War: betraying the other Roman houses and installing myself as Emperor, overthrowing the Roman Republic in the process, assassinating potentially dangerous Generals and agents from allied factions, cracking down on any kind of provincial dissent with overwhelmingly strong garrisons, crucifying the populations of captured settlements who tried my patience, pillaging and raping as the Germanic tribes....
Medieval Total War 2: exterminating the populations of any settlements who resisted besiegement, wiping out every last Italian man, woman and child after Venice dared to betray the Holy Reich, deliberately infecting spies with the Black Death and sending them into other countries as a living biological weapon, burning innocents as heretics and witches, assassinating the Pope and installing my own puppet alongside a German dominated college of cardinals, launching Crusades against political enemies, mass executions of enemy prisoners who had the sheer gall to fight Germans, betrayal of allies who have served their purposes....(though to be fair, I've implemented a policy of having Chivalrous Generals act with compassion and mercy - had a Crusader General who conquered the Holy Lands who was the paragon of honour and morality).
Company of Heroes series: Using incendiary weapons on Allied/Soviet medical facilities, playing exclusively as the Not-Waffen SS, driving Panzers over enemy wounded, booby-trapping civilian buildings....
Dragon Age-Origins: Killing Arl Howe's entire family in revenge for his massacre of the Couslands, killing the possessed child in Redcliffe, siding with the Templars and destroying the entire Mage's Circle, siding with the werewolves and wiping out the Wild Elves, destroying the Chantry's most holy relic and killing Leliana over it, fathering a child via Morrigan purely to save my own life and then murdering her....
Fallout 3: Butchering the ghouls outside Tenpenny Towers and getting a private suite, killing everyone inside Tenpenny Towers when I was bored, nuking Megaton out of existence, working for the slavers in Paradise Falls, enslaving countless innocents for a few hundred bottlecaps each, returning to Vault 101 (I think it was) and slaughtering the inhabitants for kicking me out in the first place, pledging eternal loyalty to the Enclave (God Bless President Eden) and helping them reclaim the blasted wastes of America by purifying it of degenerate elements, poisoning the water supply with the Enhanced FEV virus, crippling the Brotherhood of Steel by killing everyone within it I could, becoming Slaver-King of Pittsburgh....(eventually I killed every single human in the game, bar the Slavers and Enclave personnel I could avoid, and then went mad from loneliness).
Fallout New Vegas: Supporting Caeser's Legion all the way and bringing order to the Mojave, infiltrating the NCR as a double-agent and rotting its Mojave position away from within, betraying everyone in the Sierra Madre, sabotaging the ghoul spaceship, annihilating entire NCR outposts by myself, convincing the Butch and Cassidy-style couple into giving up their foolish plans and handing over their special SMG, then blowing both of their heads off, having Benny crucified....
Hearts of Iron series: Leading Nazi Germany to victory in the Second World War, absorbing the Wehrmacht into the SS (by renaming every new division as an SS unit), rampaging through mainland China as Imperial Japan, breaking free of British oppression as Fascist Iraq and storming into the Caucasus in assistance to Germany's anti-Bolshevik crusade....
The way I see it, there *must* be order and stability. If a few heads must roll, and a few towns razed to the ground to see that happen, then that is a price worth paying.
Funnily enough, I'm the nicest person you'd ever wish to meet in Mass Effect (provided you haven't broken the law or fucked with anyone I care about) and I just cannot bring myself to do anything genuinely villainous in that.