In Pelles C's icon editor there is a special color named screen color and in 16 color mode a special pixel with a cross in it (not clear, how to set such a pixel).
I figured this one out by trial and error.
Scenario 1. You want to create a 16 x 16 True color + alpha channel icon from scratch:
- Create new icon in resource editor and open it in the icon editor.
- Click the "New format" icon next to the Format drop down and select "16x16 True Color + Alpha" and click OK.
You now have an empty icon filled with the special pixel.
Scenario 2. You want to add the alpha channel transparency to an existing icon:
- Open Icon in the icon editor.
- Click the "New format" icon next to the Format drop down and select "16x16 True Color + Alpha" and click OK.
- Select the original format from the Format drop-down.
- Select the non background part of the image and copy paste it into the alpha channel format you just created.
- Select the Fill too, then select the Pick Color eyedropper and sample an alpha channel pixel (with the cross). Then click the fill tool on the areas you want to change to alpha channel.
After replacing the original background with the alpha channel special pixel you can reselect and then delete the original icon format if you wish.