GUI Window on GameObject location?

You could use this:

  Vector3 pos = Camera.main.WorldToScreenPoint(unitToPopup.transform.position);
  GUI.Window(0, new Rect(pos.x, pos.y, 120, 50), CreateUnitWindow, "My Window");

You only can use the camera variable when the object to which this script is assigned is a camera or have a camera component (added, not childed!).

EDITED:
The difference from your code is the use of Camera.main instead of camera, but this will not make any difference if this script is attached to the camera.
Doing a second reading, I suppose your problem is caused by the different Y orientations between GUI and screen points: GUI Y origin is at the screen top, while screen coordinates start at the bottom. Another problem: the window top-left will be aligned to the object's center, what may not give a good result - maybe you should add some offset to make it appear above the object. Reversing the Y coordinate and adding an offset could be done this way:

// define an offset value to keep the window top above the object
public float offset = 60; //offset in pixels
  ...
  Vector3 pos = Camera.main.WorldToScreenPoint(unitToPopup.transform.position);
  // make Y coordinate run from top, and add some offset to keep it above the object
  Rect wRect = new Rect(pos.x, Screen.height-(pos.y+offset), 120, 50);
  GUI.Window(0, wRect, CreateUnitWindow, "My Window");

NOTE: WorldToScreenPoint may return a valid screen coordinate even when the object is behind the camera; if you have this problem, check if renderer.isVisible is true before rendering the window (this actually tells if the object is inside the view frustum of any camera):

  if (unitToPopup.renderer.isVisible){
    Vector3 pos = Camera.main.WorldToScreenPoint(unitToPopup.transform.position);
    ...
    GUI.Window(0, wRect, CreateUnitWindow, "My Window");
  }