Set one color transparent in texture / shader

What about something like this? I've done it for a surface shader, though you could do something similar with a fragment shader or something else. The key is that I provide a transparent colour and a threshold. If the shader detects the texture colour is too close to the transparent one, it discards the pixels. In theory, if you wanted to get cleverer you could make it modify the alpha based on closeness, then fade out elegantly as you get close to the transparent colour. Should get you started though :)

 Shader "Custom/transparent_col" {
     Properties {
         _Color ("Color", Color) = (1,1,1,1)
         _TransparentColor ("Transparent Color", Color) = (1,1,1,1)
         _Threshold ("Threshhold", Float) = 0.1
         _MainTex ("Albedo (RGB)", 2D) = "white" {}
     }
     SubShader {
         Tags { "Queue"="Transparent" "RenderType"="Transparent" }
         LOD 200
         
         CGPROGRAM
         #pragma surface surf Lambert alpha
 
         sampler2D _MainTex;
 
         struct Input {
             float2 uv_MainTex;
         };
 
         fixed4 _Color;
         fixed4 _TransparentColor;
         half _Threshold;
 
         void surf (Input IN, inout SurfaceOutput o) {
             // Read color from the texture
             half4 c = tex2D (_MainTex, IN.uv_MainTex);
             
             // Output colour will be the texture color * the vertex colour
             half4 output_col = c * _Color;
             
             //calculate the difference between the texture color and the transparent color
             //note: we use 'dot' instead of length(transparent_diff) as its faster, and
             //although it'll really give the length squared, its good enough for our purposes!
             half3 transparent_diff = c.xyz - _TransparentColor.xyz;
             half transparent_diff_squared = dot(transparent_diff,transparent_diff);
             
             //if colour is too close to the transparent one, discard it.
             //note: you could do cleverer things like fade out the alpha
             if(transparent_diff_squared < _Threshold)
                 discard;
             
             //output albedo and alpha just like a normal shader
             o.Albedo = output_col.rgb;
             o.Alpha = output_col.a;
         }
         ENDCG
     } 
     FallBack "Diffuse"
 }