Proper implementation of C# <-> Arduino serial communication

Question

I'm trying to communicate back and forth with an Arduino via serial through a C# program. I've got a basic working example, but it's not pretty and not fault-less. I've included it at the end. I have done some research online, but it's difficult to look for something when you don't know all the details and intricacies of what you're looking for.

I'm under the impression that good serial communication protocol should include a handshake, send data and wait for response, receive data and send response, data clocking, etc. My question is how best to implement this. My existing code is one-way, from C# to the arduino's serial port, and it just sends the data and assumes that it was received. It's also very simple, sending just two bytes (a 1 or 0 to turn on or off an LED, and a 0-255 to control the LED's brightness via PWM). I'd like to be able to send sensor data or confirmation that the data was received and acted on, back from the arduino to the program.

I'm also curious about syncing. Does that go hand in hand with the handshake (no pun intended)? How can I reliably send data either way and be assured that nothing will be lost due to being out of sync?

Anywho, I've rambled, sorry. Hopefully someone can shed a little learning light on this subject. Here's my current messy code:

Arduino:

#define LEDPin 9
byte SerialCmd = 0;
byte SerialVal = 0;

void setup() {
  Serial.begin(9600);
  pinMode(LEDPin, OUTPUT);
  digitalWrite(LEDPin, LOW);
}

void loop() {
  while(Serial.available() > 1) {
    SerialCmd = Serial.read();
    SerialVal = Serial.read();
    switch(SerialCmd) {
      case 0:
        digitalWrite(LEDPin, LOW);
        break;
      case 1:
        analogWrite(LEDPin, SerialVal);
        break;
    }
  }
}

C#:

using System;
using System.Windows.Forms;

namespace ArduinoTest2
{
    public partial class Form1 : Form
    {
        byte[] SerialData = new byte[] { 0, 0 };

        public Form1()
        {
            InitializeComponent();
            serialPort1.PortName = "COM3";
            serialPort1.BaudRate = 9600;
            serialPort1.Open();
        }

        public void SerialWrite()
        {
            serialPort1.Write(SerialData, 0, 2);
        }

        private void button1_Click(object sender, EventArgs e)
        {
            SerialData[0] = 1;
            SerialWrite();
        }

        private void button2_Click(object sender, EventArgs e)
        {
            SerialData[0] = 0;
            SerialWrite();
        }

        private void trackBar1_Scroll(object sender, EventArgs e)
        {
            SerialData[1] = Convert.ToByte(trackBar1.Value);
            label1.Text = trackBar1.Value.ToString();
            SerialWrite();
        }

        private void Form1_FormClosing(object sender, FormClosingEventArgs e)
        {
            serialPort1.Close();
        }
    }
}