Well, there are some minor-ingame differences. For example, making Dark Side choices often result in you going somewhere to kill more people (more XP from extra mobs) and Light Side can some times avoid a fight (So you progress faster in your quest chain but earn slightly less XP) BUT. That's not always the case, some times the Dark Choice will have you kill an extra NPC during a dialogue, which wont earn you any extra XP. And Light Choice sometimes the other character will refuse your idea and you'll have to kill them. (Yay )
Overall it doesn't change much, I guess the biggest ''difference'' is your companions (If they like or dislike your choices) But in the end, it doesn't really affect anything in the game.
PS: If EA / Bioware ever change the class story lines, I think it'd be great to have those choices affecting the story. Right now the only thing it changes is ''X companion approves.... Y Companion disapproves....) Which is kind of... meh.
