Yes, this is possible with VBA. Here is an example:

Sub FlipColor(oShp As Shape)
   If oShp.Fill.ForeColor.RGB = vbBlue Then
       oShp.Fill.ForeColor.RGB = vbRed
   Else
       oShp.Fill.ForeColor.RGB = vbBlue
   End If
End Sub

Assign this macro to a shape and each time you click it, it will change
alternate between blue and red.

--David

This makes sense, then.  So long as you understand that a VBA solution won't work in
the free Viewer, but it doesn't sound as though that's an issue in your situation.

So, add this macro and assign it to each shape whose color you want to "flip" as an
action setting.  Set the color of the shape to whatever color you've defined as the
default color.

We could probably take it a step beyond and teach it to work with any clicked shape
and remember the shape's original color, then set it back on re-click if need be.

Sub FlipColors(oSh as Shape)

Dim lDefaultColor as Long
Dim lHighlightColor as Long

' Edit these as needed
lDefaultColor = RGB(0,0,255)      ' pure blue
lHightlightColor = RGB(255,255,0)  ' yellow

With oSh.Fill.ForeColor

 Select Case .RGB
  Case lDefaultColor
     .RGB = lHighlightColor
     
  Case lHighlightColor
     .RGB = lDefaultColor
 End Select

End With

End Sub

End Sub

Round two:

Highlight shapes in PowerPoint
http://www.rdpslides.com/pptfaq/FAQ00798.htm

This one remembers the original shape's color and sets it back to that (which also
means that you don't have to set the shape to any particular color to make it work
in the first place).

And because PPT won't let you assign macros to multiple selected shapes at a time,
there's this:

Assign an Action Setting, Run Macro action to multiple shapes at once
http://www.rdpslides.com/pptfaq/FAQ00799.htm

-----------------------------------------
Steve Rindsberg, PPT MVP
PPT FAQ:  www.pptfaq.com
PPTools:  www.pptools.com
================================================