Every gameworld will have its own origin for Good and Evil. It should be different for EVERY GAMESETTING. There is no one source. It is one of the fundemental parts of every mythology. Even if there is not a religion per say, there will be a story about Good and Evil.
Of course, the story might have absolutely nothing to do with the actual origin, but it is what people believe.
The Greeks through Evil was part of the world, innately... though eventually Titans were blamed for it. But I digress.
In worlds of obedience or power, (i.e. you follow your dieties not because of faith but in fear of what happens when you don't do what they say OR you believe in them because of the power/ spells/ miracles/ they grant), the definition of Good Powers and Bad Powers is a little more clear cut - kind of like the teams on a football field. You are what you get from your "higher power". Given the existance of powers, there might be a clear cut story behind Good and Evil.
Those powers may or may not give their clerics their view upon the sources of good or evil. If they don't, the clerics of centuries gone by will have probably made something up to explain it all. By the time the players are running around, those parables have become dogma and mythology.
Now in a euro medival fantasy of the Tolkein mold (i.e. most fantasy games based upon DnD), the teams are automatically set up. Good gets good powers and Evil gets their powers. The actual origins are mere windowdressing to explain why they two antagonistic sides exist.
In a more game orriented view, without Evils there is nobody for Good to "beat up" and "take their stuff". And of course, Evil imperils the world... Good must stop Evil... the quest continues. So there must be a Good and Evil. There might even be a story that actually impacts the way the world is and defines Good and Evil's goals, but normally there is nothing there.
I mean, how often do you actually think about how Good and Evil came to be in your own mythology (If you are a Christian, Jew, Moslem, Wicca, Buddhist, Taoist, Shintoist, or Confussionist). How often does someone's belief in that story impact the world?
Of course, some games do not run Good vs Evil. RuneQuest/ HeroQuest and Glorantha Setting ignores Good and Evil as Order and Chaos are the big opposing polarities. Many Asian settings ignore Good and Evil and concentrate on Being in Way with the flow of the world or being in opposition of said Way.