Metal Gear Solid Series (zero kill run confirmed in MGS4)

The Metal Gear Solid series has been noted for a historic role popularizing stealth gameplay, and sometimes giving players the option of avoiding a surprising number of kills— considering that the protagonist "Sold Snake" is an elite military specialist of some sort, in the business of infiltrating high-tech strongholds full of enemy combatants.
Box art for the original 1987 Metal Gear release
By most accounts, it sounds as though the entire series belongs on the "Pacifist Challenge Run" list, and the 2008 "Metal Gear Solid 4: Guns of the Patriots" has been confirmed to be winnable as a perfect zero kill run.
Metal Gear Solid 4: Guns of the Patriots is a confirmed zero kill run game
With the caveat that we're relying on third-party information, these are the rumored prospects for each entry in the Metal Gear Solid franchise:

Metal Gear Solid reportedly gave players the option to knock out foes like guards without killing them, but at minimum still required players to have to bump off some of the bosses to get through the whole game.

Metal Gear Solid 2 introduced a new asset that made it even less mandatory to kill enemies: Possibly taking the hint provided long ago by the 1980's Sega arcade game "Tranquilizer Gun," the game gave players just such a weapon, making it possible to eliminate all but two enemies (both bosses) by tranquilizing them.

Metal Gear Solid 3 apparently raised the bar by making it possible to defeat all bosses without kills, but apparently still caused a "scripted kill" to take place, in which the game's lead character kills one of them (even if the player had already exerted the effort to defeat them with non-lethal methods).

Finally, however, 2008's Metal Gear Solid 4 raised the bar even higher and became the first genuine zero kill run Metal Gear Solid game, in which players could win the entire game without bumping off even a single boss with lethal means.

In addition to lots of stealth gameplay and nonlethal weapons, Metal Gear Solid 4 offers players some very cool-sounding nonviolent assets such as an OctoCamo suit to mimic the appearance of surface textures to evade detection, and even a FaceCamo to mimic the faces of other characters in the game.
Snake climbs into a dumpster to hide from enemies, a great new addition to any player's list of nonviolent tactics...
An even more unusual addition to the game is the "psyche meter," which The Metal Gear Solid 4 Wikipedia article describes like this: "A further addition to gameplay mechanics is the Psyche Meter. Psyche is decreased by non-lethal attacks, and is influenced by battlefield psychology. Stressors (including temperature extremes, foul smells, and being hunted by the enemy) increase Snake's stress gauge, eventually depleting his Psyche. Adverse effects include difficulty in aiming, more frequent back pain and the possibility of Snake passing out upon receiving damage. Among the available methods of restoring Psyche are eating, drinking, smoking, and reading an adult magazine."
Snake boosts his psyche meter between missions, while the game engine warns that MGS4 was intended exclusively for use with the PS3...
Apparently the Metal Gear series was developed by Hideo Kojima, the same designer who created "Snatcher," and includes the excellent addition of a "support robot" to accompany the player (which was also one of the fun features in Snatcher, in which the robot buddy was named "Metal Gear").
Apparently Kojima had already publicly announced that he wanted to retire after directing Metal Gear Solid 3, but was persuaded to return for MGS4 after what Wikipedia described as "substantial negative fan reaction, including death threats."
Snake plays dead, another nice new addition to the nonviolent tactics list. May also come in handy if the gunman in the background is one of the Metal Gear Solid fans who allegedly issued death threats in response to rumored changes to the series...
Metal Gear Solid 4 was (as far as we know) exclusive to the Playstation 3, so maybe we'll have to pick one up someday, since just a glance at the Wikipedia article is enough to make the ardent "pacifist challenger" want to give the game a try.