What enemy have you felt bad about killing?

[Blow_Pop]

The flying dragon/snake in Shadow of the Colossus. It was just so peacefully flying around above me and wasn't trying to hurt me even when I did hit it with an arrow.......

 

[TheGreatCoolEnergy]

NO BECAUSE IT IS A STUPID VIDEO GAME, NOT REAL LIFE.

Good art is supposed to shock and stun it's audience, and leave an impression on their morality, if only for a little while. And the fact that video games are interactive just makes them more immersive

 

[War Penguin]

All of them. It's a sad day when I play a game.
Seriously, though, any enemy in Pikmin. Everything there is just so cute... and vicious.

ahh Pikmin. So loyal. One time I brought all my red into a field, without knowing that there was some monster there. It popped out of the ground and just killed all of my Pikmin. I felt kinda bad as I had just walked them to their death.

Yeah, that's the thing with Pikmin. You (or at least I) get so attached to your viciously cute minions that it's painful to watch them die. But then you reload your game and everything is fine.

 

[DeathWyrmNexus]

Ah, I had forgotten about Saint's Row 2 and Julius. Maero and Jessica had it coming being as I owned 2/3 of the city when they treated me like a peasant child. I did feel bad about Julius since I never played SR 1 to even be pissed at Julius. :/

 

[badgersprite]

Oblivion. Dark Brotherhood Quests.

Spoiler

All the Dark Brotherhood characters in Cheydinhal. They were easily the most fleshed out NPCs in the entire game. Plus, you know...I was their sister, and Vicente sired me, and Mraaj Daar had finally warmed up to me. And they were all innocent. I felt horrible. =(

I take your definition of "innocence" is a bit off, but anyway, I felt the same about killing them.

Well, they weren't traitors, anyway.