For me it is all about immersion. If I feel like the actions of my character are a driving force of the story, and I can actually identify with the character then I will choose to be good/paragon/whatever ... really the only game I have done this for was Mass Effect series (also has to do with the fact that your choices have a lasting impact that will affect not just the game you are playing but also the sequels).

Most games I find myself going evil though ... seems to have the best perks and the best looking armor/weapons. Besides, virtually every video game I have ever played with some form of moral choice system really does not punish you in any lasting way for being evil. In real life, murder and theft are obviously highly irrational behaviors because people in all societies will not tolerate such behavior (there is also the obvious emotional consequences of killing and stealing), but in video games these rules do not apply.

For example, I can kill a whole town full of people in Skyrim and rob them in the process, and all I will have to do is go to the jail for 30 seconds and I will be back out on the street a minute after the massacre. I don't really feel all that bad for killing a bunch of ones and zeroes really since (in most games) the vast majority of NPCs are not characterized well enough for me to feel any kind of loss. 

Morality, to me at least, should be practical. I suppose you could follow some kind of moral code "just because," but I don't see the logic in it. In Mass Effect at least my character has a reputation that I am roleplaying, and evil actions while not damaging in a gameplay sense would still alienate me from the character I have built and grown to enjoy. Thus, it makes sense for me to "do the right thing" because it effects my overall enjoyement of the game.

It would be interesting to see a game that actually punished the player in a real lasting way for their actions, but developers would have to be creative about it. If the punishments are too drastic then the player will get frustrated and be removed from the experience, but if the punishments are too lax (as is mostly the case) then the moral choices loose all impact.