Displaying MPO 3D images does not work properly in Geeqie 1.1.
To display 3D photos correctly, the left and right picture have to be shifted a few pixels against each others. The value to do that is stored in a Tag "Parallax" in the embedded MPF section of MPO files. This parallax tag can be read by ExifTool.
exiftool -ee -b -Parallax source.MPO
To calculate the shift between both images:
parallax-shift = image-width / 100 * parallax-value
The parallax shift can be used to improve the viewing quality of 3D images.