Has a game ever...

[MisterShine]

The clearest one I can remember would be in Vampire: The Masquerade.

At one point in the game you are captured by a corporation/paramilitary group that experiments on you to figure out what myths on vampires are truth or bullshit. The first few tests are fire, electricity, gas, but then one test is just a guy holding up a cross. After seeing it not affect you, he drops the cross and runs screaming. The game will not let you proceed until you kill him. Why would I attack him? I played a more-or-less good guy to that point, why do I want to kill him? He could've just been some poor schmuck who pissed off the boss and had no idea what was going on. Clearly wasn't a threat at all...

I feel bad every playthrough.

 

[Serenegoose]

In pretty much any game where there's a choice I feel a little bad for killing the enemies. Like in Iji, the main character apologises the first few times you kill them, and given I could have just passed them by, it felt a little guilt inducing.

 

[Roperius]

Red Dead Redemption made a very good effort in Undead Nightmare; plenty of developed characters turned into zombies who you have to 'off.'

There's also quite a good quest involving a certain mythical creature... I shan't say, through fear of revealing spoilers.

 

[Grubnar]

World in Conflict: Soviet Assault had many moments where the futility and utter stupidity of war was laid bare. It is not often I have CARED so much when playing a videogame.

And there was a moment in Battlefield: Bad Company 2 single player campaign where I felt the same way.

 

[flying_whimsy]

I really felt bad for killing anything in shadow of the colossus: from the big beasties to the little lizards. By the end when I thought I'd been desensitized enough (and admittedly was pretty vindictive after the final colossus) the end credits went and made me feel really terrible all over again. Stupid credits. Stupid murderous me.

EDIT: Actually, the whole killing in games has been getting to me a lot lately. I've been playing more abstract and puzzle based games just because I'm getting tired of killing things. I hadn't really realized I was having a problem until I watched the Rebecca Mayes video for Batman: Arkham Asylum. I'm tired of killing. I'm also getting tired of rolling up the same katamaris because I can't figure out what else to play.

 

[No_Remainders]

... Does blowing the shit out of Megaton count?

I mean, they weren't really my enemies..

Until I decided to steal all their stuff.

 

[Nannernade]

A game is supposed to do that? Since there isn't a make them feel bad about what they're doing button... killing is the only thing that makes sense.

 

[Doclector]

The collosuses (collosi?) from shadow of the collossus. Barely any of them actively attack you until you attack them.

 

[magicmonkeybars]

The clearest one I can remember would be in Vampire: The Masquerade.

At one point in the game you are captured by a corporation/paramilitary group that experiments on you to figure out what myths on vampires are truth or bullshit. The first few tests are fire, electricity, gas, but then one test is just a guy holding up a cross. After seeing it not affect you, he drops the cross and runs screaming. The game will not let you proceed until you kill him. Why would I attack him? I played a more-or-less good guy to that point, why do I want to kill him? He could've just been some poor schmuck who pissed off the boss and had no idea what was going on. Clearly wasn't a threat at all...

I feel bad every playthrough.

I never got that, I guess I was too deeply ingrained into the beastial nature of my PC to care about one poor bastard who signed up with the wrong people. (I tend to play as a Gangrel)

OT I guess I have felt regret/reluctance but I can't think of a specific example.
Usually npcs that beg and plead for life have a bigger impact on my heart strings than regular armed enemies.

 

[CharrHearted]

Heavy rain anyone? I couldn't bring myself to shooting that man to get an extra letter to the location of Sean Mars. This man was a drug dealer... but he had children. He might have been cruel to them... but he's actually innocent if you follow the scene in a different way. In the end I accidently hit the R2 button, Ethan put a gun to the drug dealers head... and shot him. I looked down in disgust thinking about what drove me to kill a man just to save my son. He didn't deserve it, and I would grieve for the fathers daughters... It was all my fault. And what was it all for... A single bloody letter.

 

[Nieroshai]

There was something I did myself that I felt bad about. WoW has an achievement for /love -ing critters around Azeroth. Some of those creatures are also part of an achievement for killing pests. So I found myself saying "I love you" to a rabbit, right before plunging my spear into its intestines. It sounds even worse when I say that out loud...

Also, my happiest moment was when I adopted my first vanity pet. It was a cat-sized plague grub I found in a sack. For some reason, I find it somewhat adorable...

 

[binvjoh]

Deus Ex. Trying to be the good guy isn't always easy.

 

[Nostalgia Ripoff]

In Fallout, I generally try to do as little killing as possible. After all, they're never coming back in that game.

 

[superstringz]

Iji. First Time through, I was psychopathic in my killing the Tasen/Kamoto, refusing to move on until EVERYONE was dead. After all, these guys wiped out my planet, so why shouldn't I get revenge... Except if you play the monster, they treat you like a monster, and Iji starts acting like a huge ham, which left a bad taste in my mouth. Playing through as an actual pacifist the second time through was more satisfying.

 

[tahrey]

Huh... makes me feel a teensy bit sociopathic now... but then games are where my hatred of all the stupid shits in the world comes out

Like, if I'm playing an air combat game, there should maybe be a touch of nemesis cameraderie between myself and the opposing pilots ... we're really just doing our jobs, and it's the same jobs. Except usually they're the defending force, they're trying to protect their homeland (crap and badly ruled as it may be) and I'm the murderous intruder. Similarly the guys in the radar and missile bases or whatever that I blow up (and the storage depots... not so much the terrorist-seized bases, though)... they're probably civs, yknow...

Nah.

Shoot up an enemy jet, and the pilot manages to luck out and eject before his plane goes boom? Quick 180 flip turn and CANNON CANNON CANNON at the speck underneath the descending canopy. Take that you bastard... and whilst I'm at it, let's shoot up the mobile SAM operators clustered around the already-exploded radar base, even though they haven't got any way of firing at me any more.

Bit worse when I was an evil little shit, er I mean, a child, of course. Not played so many of the games which offer that particular type of scenario of late. Though I did struggle through about an hour of Shadow of the Colossus, before giving up in a mixture of "how the hell are you supposed to do this?", "WHY the hell am I doing this?" and "...that big monster thing was just having a boring old day, not hurting anyone before I turned up to ruin his shit. My protagonist is a dick".

 

[Snotnarok]

Nope, never to be quite honest. I know it's a virtual world so I don't care who gets a bullet/sword/knife/arrow in their head.

 

[Okuu_Fusion]

Undead Nightmare made me feel bad for killing sasquatches...

Even though you don't kill your enemies, always feel bad about beating the crap out of Reisen in the Touhou fighters...

 

[oreopizza47]

The Nihilanth out of Half-Life 1. I felt so sorry for two reasons: 1) It was plain to tell that he/she/it didn't really want to do it, but the whole planet was pretty much being controlled by the Combine and 2) I felt kind of crappy for using codes to blast right through his alien-baby face.