Note. Unity 5 introduced the Standard Shader which replaces these shaders.
The Transparent shaders are used for fully- or semi-transparent objects. Using the alpha channel of the Base texture, you can determine areas of the object which can be more or less transparent than others. This can create a great effect for glass, HUD interfaces, or sci-fi effects.
Is something described here not working as you expect it to? It might be a Known Issue. Please check with the Issue Tracker at issuetracker.unity3d.com.
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