Shader based texture painting. Add the script to a plane with a collider and attach a render texture

PaintCloudData.shader

Shader "NewChromantics/PaintCloudData"
{
	Properties
	{
		_MainTex ("Texture", 2D) = "white" {}
		PaintUv("PaintUv", VECTOR) = (0,0,0,0)
		PaintBrushSize("PaintBrushSize", Range(0,0.1) ) = 0.1
	}
	SubShader
	{
		Tags { "RenderType"="Opaque" }
		LOD 100

		Pass
		{
			CGPROGRAM
			#pragma vertex vert
			#pragma fragment frag
			
			#include "UnityCG.cginc"
			#include "CloudData.cginc"


			struct appdata
			{
				float4 vertex : POSITION;
				float2 uv : TEXCOORD0;
			};

			struct v2f
			{
				float2 uv : TEXCOORD0;
				float4 vertex : SV_POSITION;
			};

			sampler2D _MainTex;
			float4 _MainTex_ST;
			float PaintBrushSize;
			float2 PaintUv;
	
			
			v2f vert (appdata v)
			{
				v2f o;
				o.vertex = mul(UNITY_MATRIX_MVP, v.vertex);
				o.uv = TRANSFORM_TEX(v.uv, _MainTex);
				return o;
			}
			

			fixed4 frag (v2f i) : SV_Target
			{
				uint3 CloudDataPos = GetCubeDataPos( i.uv );

				if ( distance( i.uv, PaintUv ) < PaintBrushSize )
					return float4(0,0,0,1);
				return tex2D( _MainTex, i.uv );
				return float4(1,0,0,1);
			}
			ENDCG
		}
	}
}

PaintMe.cs

using UnityEngine;
using System.Collections;

public class PaintMe : MonoBehaviour {

	public Material PaintShader;
	public RenderTexture PaintTarget;
	public RenderTexture TempRenderTarget;

	// Use this for initialization
	void Start () {
	
	}
	
	// Update is called once per frame
	void Update () {

		RaycastHit hitInfo = new RaycastHit();
		Ray ray = Camera.main.ScreenPointToRay(Input.mousePosition);

		// OnMouseDown
		if (Input.GetMouseButton(0))
		{
			if (Physics.Raycast(ray, out hitInfo))
			{
				hitInfo.collider.SendMessage("HandleClick", hitInfo, SendMessageOptions.DontRequireReceiver);
			}
		}

	}

//	void OnMouseDown()

	void HandleClick(RaycastHit Hit)
	{
		var LocalHit = transform.worldToLocalMatrix * Hit.point;
		var LocalHit3 = new Vector3(LocalHit.x, LocalHit.y, LocalHit.z);
		LocalHit3.Scale(transform.localScale);
		print("Box Clicked at " + LocalHit3);

		//	transform to uv
		Vector2 LocalHit2 = new Vector2();
		LocalHit2.x = 1- (LocalHit3.x + 0.5f);
		LocalHit2.y = 1- (LocalHit3.z + 0.5f);

		PaintAt(LocalHit2);
	}


	void PaintAt(Vector2 Uv)
	{
		Debug.Log("Paint at " + Uv);
		if ( TempRenderTarget == null )
		{
			TempRenderTarget = new RenderTexture(PaintTarget.width, PaintTarget.height, 0);
		}
		PaintShader.SetVector("PaintUv", Uv);
		Graphics.Blit(PaintTarget, TempRenderTarget);
		Graphics.Blit(TempRenderTarget,PaintTarget, PaintShader);
	}
}