I was originally passing on this question, as I feel there are far more important qualities to color choice beyond traditional moral delineations in mainstream American media, such as cultural meanings, historical meanings, theme and "look and feel" of the fiction, color blindness, usability, and more. However, if what is truly desired is a "common" perception of good, evil, and neutrality, then:
Every hue has positive associations, but blue and green are almost universally positive, being the colors of a clear sky and plant life. Any habitable land on a temperate day will flourish with blues and greens.
Red has significant negative correlations that transcend culture, largely due to the color of human blood. While doctors and healthcare are often associated with red, so are wounds and recent deaths which can be more universal and pervasive.
Yellow and Orange are unusual colors with multiple positive and negative assocations, especially the association with fire, which can be vital to survival and deadly when uncontrolled. This is why there is often a "neutral" valuation with such colors.
Lighter and brighter colors are often associated with "good". Bright light is the reason for this, as all colors are lighter and brighter on a clear day. Note that "white" is not necessarily associated with daytime, merely with the absence of night, which is one reason why "white" can have very different associations depending on culture.
Conversely, darker and more desaturated colors are associated with "bad". Darkness is the clear association here, as darkness conveys the unknown and unknowable. For the same reason one is much more likely to be scared of the dark than to be scared of the clear daytime, so are darker or greyer colors more likely to evoke negative associations. Black of course is the color of complete darkness, the elimination of the primary sense our species uses, resulting in a color easily associated with negativity, fear, death, and more.
Conclusion regarding the question of "What is the most common representation in games?"
The most common associations would be one of a few alternatives.
- The classic "blue vs red", with some yellow, grey, or other color for "neutral". A common example of this is Star Wars.
- Green, Yellow, and Red, commonly associated with "Go" "Caution" and "Stop", or stoplights. This extends beyond pure gamer or sci-fi/fantasy culture to many drivers across the world (I'm unaware of any nation/culture that doesn't use this scheme for stoplights)
- Any colors of differing brightness and saturation. You could even use the same hue, as long as the bright and light color represented "Good", a darker and dimmer color was "Neutral", and even darker and greyer was "Bad"/"Evil".
- Combine the associations with hue and saturation with a bright blue and green as "Good", a neutral valued yellow and orange as "Neutral", and either a dark or desaturated red as "Evil"/"Bad", probably combined with "Black" to give you your desired 6 colors, though if you really wanted to stick to colors with actual hues, a dark or desaturated color of any hue would fit in well enough with the rest of the scheme. Yellow could also work, but would leave you short a common "neutral" color.