In order for a moral choice to have weight, it needs to have two components. First, meaningful choices have to cause the player to lose something in order to gain power. Something has to change, or be expected to change, within the game in order for the decision to matter. In Mass Effect, at one point in the game, you have to choose which of two party members to rescue – the other dies. Or, in Fallout: New Vegas, working with Caesar's Legion turns the New California Republic into an enemy, and vice versa.
Second, a moral choice has to be a difficult choice. The old adage "If doing the right thing were easy, everyone would do it" applies here. This is where games usually fail. They can do it with little choices, like with stealing even when you won't get caught in New Vegas. Take the owned items and you'll lose karma, which might be a small hit compared to the benefits of a new weapon. Alternately, in some games, honorable characters will simply refuse payment for quests, forcing money to be acquired by other means.
