ProtocolController.cs

using Microsoft.Win32;
using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Text;
using System.Threading.Tasks;

namespace MyNamespace
{
    public class ProtocolController
    {
        public static readonly string ExecutingAssemblyLocation = System.Reflection.Assembly.GetExecutingAssembly().Location;

        public string Protocol { get; set; }

        public Dictionary<string, Action<Dictionary<string, string>>> Actions { get; set; }

        public ProtocolController(string protocol)
        {
            this.Protocol = protocol;
            this.Actions = new Dictionary<string, Action<Dictionary<string, string>>>();
        }

        private void RegisterProtocol()
        {
            try
            {
                RegistryKey regKey = Registry.ClassesRoot.CreateSubKey(this.Protocol);
                regKey.SetValue("", "URL:" + this.Protocol + " Protocol");
                regKey.SetValue("URL Protocol", "");

                RegistryKey defaultIcon = regKey.CreateSubKey("DefaultIcon");
                defaultIcon.SetValue("", Path.GetFileName(ExecutingAssemblyLocation));

                regKey.CreateSubKey("shell")
                      .CreateSubKey("open")
                      .CreateSubKey("command")
                      .SetValue("", ExecutingAssemblyLocation + " %1");
            }
            catch (UnauthorizedAccessException)
            {
                Console.WriteLine("ERRO");
                throw;
            }
        }

        private void RunUrl(string url)
        {
            url = url.ToLower();

            var uri = new Uri(url);
            var protocol = uri.Scheme;
            var action = uri.LocalPath;
            var parameters = uri.Query.Remove(0, 1).Split('&').ToDictionary(x => x.Split('=')[0], x => x.Split('=')[1]);

            this.Actions[action](parameters);
        }

        public void Run()
        {
            Console.WriteLine("running " + this.Protocol);

            var arguments = Environment.GetCommandLineArgs();

            if (arguments.Length > 1 && arguments[1].Contains(this.Protocol))
            {
                Console.WriteLine("running " + arguments[1]);
                RunUrl(arguments[1]);
            }
            else
            {
                Console.WriteLine("Instalando");

                RegisterProtocol();

                Console.WriteLine("Instalado com sucesso");
            }
        }
    }
}

Usage

var controller = new ProtocolController("myprotocol");

//myprotocol:myaction?email=asd@qwe.com
controller.Actions.Add("myaction", p => Console.WriteLine(p["email"])); 

controller.Run();