Pure Liquid Malevolence

 Evil will always triumph, because good is dumb.

That's actually only true in video games, though. In reality, evil is firstly incredibly hard to define (what with the specifics of morality varying from culture to culture and person to person) and secondly, typically antisocial. Refusing to cooperate with your peers forces you into a serious handicap, while others can draw on the resources of their allies to get ahead.

The most useless moral choice system is probably the prototypical Fable model - where random, unmotivated and inconsequential acts of either sadism or kindness create purely aesthetic effects on the player character. The system literally might as well just not exist - it would have no impact on the gameplay.

A step up from this is the BioShock model, where specific moral choice events that occur lead to differing consequences. Depending on how this is handled, it can be just as useless as the Fable system, or even worse (particularly if your moral choices arbitrarily block your access to sets of abilities, which removes morality from the situation altogether, making it just a stat-building choice instead). BioShock itself does an okay job of replicating the real-world scenario, though. The 'evil' course of action leads to immediate rewards, while the 'good' action is a longer-term strategy that relies on mutual cooperation with the Tenenbaum character. In most practical situations, the evil course of action would be coupled with some negative consequence, but given that most everyone in the city of Rapture is already your enemy, it makes sense that you don't lose much by acting like a bastard.

Then we have the real winners: games like the old classic Planescape: Torment, which don't have an explicit moral choice system, but instead just treat the player to the real benefits and consequences of their actions. Being a bastard is usually a bad idea; there is much more personal profit to be earned from cooperating with the NPCs to a mutual end. Mistreating, injuring, or killing them still produces benefit, even if nothing more than in the form of stolen money, but this is typically sub-par. Better yet, some of the game's areas have proper governing bodies and police forces, so rampant criminal activity will lead to severe negative consequences - just like it should in real life. If you want to be a crook, you have to learn how to manage it while dodging the cops.

Moral choice constructs made a fair effort to try to introduce some meaning to the games where they appear, but it's the fact that they are as simple and artificial as they are that ruins them. Proper "morality" is complex, nuanced, and incorporates shades of grey that can't be represented with a simple score. Better to drop the "moral" choice and just have choice - along with the reasonable, logical consequences that would come with choice. Do that well, and the morality content will appear on its own.