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So what exactly did I do? I made sure that different colors had different opacities that matched the nature of their color as they would in reality. Here's an extreme example:

The simple answer is that the white is a milkier pigment and most of the overall light shone through it gets absorbed, while light shining through orange pigment would just transform the light into orange light by blocking some and letting in other parts of the spectrum. You'd also expect a black tint to block out more overall light. So how do you figure out which color needs which opacity, since white and black couldn't be any more opposite, why are they less translucent than orange? What about red or yellow, are they more or less transparent than orange? The deceptively complex answer is that lighter colors reflect more light from your side by blocking light from the other and darker colors absorb more light from your side by blocking light from the other--the difference is in the specularity of the pigment and the intensity is in the concentration of the pigment.

For translating this to something I could actually use I turned to the logic used behind the design in BetterGlass. The overlay blend mode on Better glass essentially works by setting up a threshold in the color so that all colors darker than middle grey (rgb: 128,128,128) are multiplied with the colors behind them and any color lighter is screen blended with the colors behind them. Obviously you can't do anything like this in vanilla Minecraft, but this was the ultimate logic I used for determining opacity of each color. (Other tests were done, but this yielded the best result.) So how do you make use of this?

Well, first you need to come up with the colors you're using to tint your glass with. For this I took my averaged cloth block colors and applied some filters that increased their saturation and brightness depending on a variety of factors, as well as mixing them in with pure value hues. How I got my final colors is not that important since you can come up with whatever colors you want from scratch that you think will look good. Once I had my colors though, I lined them all up as an image of the complete palette. Then I did some calculations and determinations of how the above opacity logic would apply to each color mathematically. The procedure is as follows:

1. Desaturate the image completely (make it greyscale).

2. Duplicate the image as a second layer and invert it's colors.

3. Set the blend mode to Difference (this will make colors darker than middle grey invert their shade so that the darkest colors are now also the lightest and the lightest colors remain the lightest)

4. Eyedrop sample the RGB grey color value (0-255), This value is your opacity factor. The higher the color, the more opaque the glass.

5. Do any final post-process calculations on the values for each color for your glass-coloring rig. (I used (X-128)*.0.788, your calculation should vary based on your glass creation rig.)

At first glance it doesn't look like there's anything weird or different about them, but that's actually the sign that you did it correctly. Even though all colors have a different opacity than their neighbor, your brain sees them as it would in reality and you detect nothing unusual. Pigments in actual stained glass would also do this with lighter colors tending to be more opaque due to their milkiness, and darker colors tending to block more light. In reality the mechanics would actually be a bit more complex than this, but as far as vanilla Minecraft goes, this is the best you can get.

This is using Minecraft's custom block models.

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