The game Deus Ex (Wikipedia) by Eidos Interactive, released in North America on June 26, 2000, had very different results based on player moral decisions in three areas: conversations with other characters; direct actions in the physical world of the game; and choices of specialization area in the attributes of the character's advancement.
For instance, in one action-based moral decision, the player has to decide whether or not to kill an "ally" who is threatening to kill another character that the player may be sympathetic to, and whose faction the player will eventually join (thus becoming an enemy of the purported "ally" who is doing the threatening). The player can survive the conflict and proceed in the game regardless of whether or not the player prevents their purported "ally" from killing the one they are threatening, but the player's choice will have consequences of a moral nature. (For those familiar with the game, the reference here is the Anna Navarre vs. Jaime Lebedev scene).
The player can also assign various skills and attributes to their character as part of play advancement. The "points" needed for the player to select these attributes are doled out in such a way that players are forced to specialize in particular areas, and cannot become a master of all. For example, the player can choose to specialize in stealth, by developing skills and choosing augmentations that allow the player to sneak past enemies without directly confronting them. This play style causes the player to be able to avoid enemy casualties, which has direct moral consequences when the player deals with other characters in the game. By contrast, if the player specializes in abilities that further the player's ability to kill enemies, such as better accuracy and damage with rifles, the player will likely not have enough points left over to also be stealthy, and will thus reap the moral consequences of killing more enemies (which could sometimes be by necessity in some situations where special stealth abilities are required to avoid a conflict and progress in the game).
Finally, the player is given moral decisions from the very beginning of the game through the culmination in the end, via dialogue. The player can choose to help people or to ignore, confront, or even kill them. Sometimes these people may be perfectly innocent, and sometimes they may be devious and attempting to deceive or take advantage of the player. This aspect I feel is even more common in video games both prior and since, compared to the other two moral aspects of Deus Ex.