Put a program in the system tray at startup

If you are using a NotifyIcon, try changing ShowInTaskbar to false.

To remove it from the Alt+Tab screen, try changing your window border style; I believe some of the tool-window styles don't appear...

something like:

using System;
using System.Windows.Forms;
class MyForm : Form
{
    NotifyIcon sysTray;

    MyForm()
    {
        sysTray = new NotifyIcon();
        sysTray.Icon = System.Drawing.SystemIcons.Asterisk;
        sysTray.Visible = true;
        sysTray.Text = "Hi there";
        sysTray.MouseClick += delegate { MessageBox.Show("Boo!"); };

        ShowInTaskbar = false;
        FormBorderStyle = FormBorderStyle.SizableToolWindow;
        Opacity = 0;
        WindowState = FormWindowState.Minimized;
    }

    [STAThread]
    static void Main()
    {
        Application.EnableVisualStyles();
        Application.Run(new MyForm());
    }
}

If it still appears in the Alt+Tab, you can change the window styles through p/invoke (a bit hackier):

protected override void OnLoad(EventArgs e)
{
    base.OnLoad(e);
    IntPtr handle = this.Handle;
    int currentStyle = GetWindowLong(handle, GWL_EXSTYLE);
    SetWindowLong(handle, GWL_EXSTYLE, currentStyle | WS_EX_TOOLWINDOW);
}
private const int GWL_EXSTYLE = -20, WS_EX_TOOLWINDOW = 0x00000080;
[System.Runtime.InteropServices.DllImport("user32.dll")]
private static extern int SetWindowLong(IntPtr window, int index, int value);
[System.Runtime.InteropServices.DllImport("user32.dll")]
private static extern int GetWindowLong(IntPtr window, int index);

In your main program you probably have a line of the form:

Application.Run(new Form1());

This will force the form to be shown. You will need to create the form but not pass it to Application.Run:

Form1 form = new Form1();
Application.Run();

Note that the program will now not terminate until you call Application.ExitThread(). It's best to do this from a handler for the FormClosed event.

private void Form1_FormClosed(object sender, FormClosedEventArgs e)
{
    Application.ExitThread();
}

As a bit of a cludge, you could configure the shortcut that launches your app to "run minimised"? That might give you what you need!

Like so: (image just an example from google)...

_{(source: unixwiz.net)}

this is how you do it

static class Program
{
    [STAThread]
    static void Main()
    {
        NotifyIcon icon = new NotifyIcon();
        icon.Icon = System.Drawing.SystemIcons.Application;
        icon.Click += delegate { MessageBox.Show("Bye!"); icon.Visible = false; Application.Exit(); };
        icon.Visible = true;
        Application.Run();
    }
}