Slight modification to the Texture Mask shader on the Unity3D wiki (http://wiki.unity3d.com/index.php?title=Texture_Mask). It multiplies the main texture's alpha channel with the mask's, so it preserves any transparency your main texture has.

MultiplicativeTextureMask.shader

Shader "MaskedTexture"
{
   Properties
   {
      _MainTex ("Base (RGB)", 2D) = "white" {}
      _Mask ("Culling Mask", 2D) = "white" {}
      _Cutoff ("Alpha cutoff", Range (0,1)) = 0.1
   }
   SubShader
   {
      Tags {"Queue"="Transparent"}
      Lighting Off
      ZWrite Off
      Blend SrcAlpha OneMinusSrcAlpha
      AlphaTest GEqual [_Cutoff]
      Pass
      {
         SetTexture [_Mask] {combine texture}
         SetTexture [_MainTex] {combine texture, previous * texture}
      }
   }
}

I wish github had shaderlab syntax highlighting :(