Depends on the game in my case, but I'm a bit of a softy in general.
I can kill random NPCs in a game like Grand Theft Auto and think little of it, perhaps because of the lack of punishment (beyond a wanted level, which, actually, is often fun), but mainly because pretty much everyone in GTA's dark, corrupt world deserves it somehow.
In games with more consequences to ones' actions (even if that's just a bad reputation), I find it hard to do evil deeds. For instance, in the first area in S.T.A.L.K.E.R.: Call of Pripyat, you can align yourself with the loner Stalkers (who are generally honest) or the bandits (who rob Stalkers and are generally complete dicks). On my last playthrough of the game I fully intended to align with the bandits (go the evil way) just to see what it was like, and despite my intentions I fell in with the stalkers anyway, I just couldn't help it.
Further, while sometimes I go after mutants with a vengeance, I often find myself feeling sorry for the blind dogs and I feel pangs of guilt when I hear them whimper after being shot. Nowadays I often find myself trying to avoid them so I don't have to kill them. Q_Q
Likewise in Deus Ex, I've always thought it might be cool to concentrate on upgrading heavy weapons skills and melee, and become a big walking tank who regards everyone with contempt, but I always end up being a stealthy mediator who solves disputes and gives starving kids candy bars.