I think it depends on the game and the characters involved in the current situation. For instance, in Chrono Trigger when you first meet Marle, I feel it's the right thing to do to show her around, immediately give her back the pendant, etc. Of course, on future plays I try to make her mad because she's annoying. Team Lucca all the way.
In Heavy Rain and/or Beyond: Two Souls, I make choices that I think would be best for the current character. If that means killing someone else or setting a house on fire, so be it.