For downloadable web software, how does one make a 3D product box and shadow as seen here? (Please ignore that it is 3 boxes.)

Have you looked for a tutorial? That would be a fairly complex drawing, and hard to cover all of it in a message reply. Short of writing out a full tutorial, I would say you'd want to use the 3D Box tool, Text tool, and Perspective extension. And I can see where you might use the Gradient tool, and some blurring as well. Possibly the Pen/Bezier or Pencil/Freehand tool in spiro spline mode, for those swooshes, and in regular mode for the dark, heavy lines. Personally, those shadows don't look very realistic, so I wouldn't draw them exactly like that. But I can see where they are fine for advertising purposes.

I have to say I'm curious why you need to draw it as a vector image, rather than just photographing the actual box? Is it because the software is downloaded, and there never will be a real box?

I wish I had time to write out a full tutorial, but unfortunately, I don't. Maybe someone else will be interested. Or maybe someone will know of an existing tutorial. Good luck

The right way to do this would be to draw the 2 (or 3) visible faces of the box, in perspective, with 2 vanishing points, (or use the to get the same result) and then use the perspective extension to map the graphic for each face to the appropriate quadrilateral. the faster but less appropriate method - and it certainly won't give the results in your example - is in the online manual here.
I made a tutorial that answers this post's question to some degree.

I found an awesome video walkthrough on this:

http://showmedo.com/videotutorials/vide ... riesID=133