<p>I made a panel and set it to fill the screen, now I can see the windows under it but I want it to be click through, meaning they could click a file or see a tool tip of another object through the transparency.</p>

<blockquote>
  <blockquote>
    <p>RE: This may be too obvious, but have you tried sending the panel to the back by right clicking and choosing "Send to Back"?</p>
  </blockquote>
</blockquote>

<p>I mean like the desktop or firefox, not something within my project.</p>

Creating a top level form that is transparent is very easy. Just make it fill the screen, or required area, and define it to have a TransparenyKey color and BackColor of the same value.
Getting it to ignore the mouse is simple enough, you just need to override the WndProc and tell the WM_HITTEST that all mouse positions are to be treated as transparent. Thus causing the mouse to interact with whatever happens to be underneath the window. Something like this...
```
```
protected override void WndProc(ref Message m)
    {
        if (m.Msg == (int)WM_NCHITTEST)
            m.Result = (IntPtr)HTTRANSPARENT;
        else
            base.WndProc(ref m);
    }
```
```