It depends on the game.
In an RPG, I'm playing a character, and I don't like it when everyone hates me. John Walker wrote an article about this once -- Bastard of the Old Republic [http://www.eurogamer.net/articles/bastard-of-the-old-republic-article] -- and I agree; one of the things that appeals to me in RPGs is the relationships you develop with NPCs, and on evil playthroughs you don't get that.
That being said, sometimes the less goodness-and-light path is the one you have to take -- recovering that one guy's body in Mass Effect is a good example; the second that politician backtalked me my girl shoved him against the wall and threatened his life, because sometimes shit needs to get done. (Not a great example -- like someone earlier said, in ME you're the good guy whether you like it or not, but still.)
Plus, every time I make an NPC sad, I feel guilty about it -- again from ME, at the beginning, if you're kind of short with the rookie you practically make him cry, and I just felt so awful for doing it, especially considering what happened next :c
On the other hand, in something like Prototype where you're really not a real person and nobody around you is a real person, ripping through the city on a glorious killing spree just makes me laugh because it's so absurdly over-the-top. So there you go.