I always try to just make choices and look at them as individual events rather than just looking at the overall picture of being good vs evil. Over the last few years, however, I've realized that this ends up being pretty boring, with the overall result of my character being a representation of the developers set of ethics, rather than my own (or just limitations with the game system).
Actually, as mediocre of an actual game as Alpha Protocol was, it certainly dis the best job I've seen of making it seem like your choices had impact and didn't just peg you outright. Coincidentally, it was one of the first games where I went in playing as a caricature (awesome spy who just lost it....or try hard who just sucked....I kind of switched halfway). And it was AWESOME. I just do that now.
But yeah, long story shot I probably end up neutral or play towards good.