The best software for 3D photo editing and processing is that created by Matsuji Suto – StereoPhoto Maker – which may be downloaded from his web page: Muttyan’s Home Page English.
This software runs only on Windows PCs. But it is also the most feature complete. It takes some time to learn to use it but after the initial learning curve, you’ll find the software does everything.
I describe how to use this software in Guide to 3D Photography (see links at upper right). There are also some tutorials available online. Perhaps in the spring time I will create some online tutorials for this too.