I am one of those group of people, who use Rhino 3D for their CAD work. Like several people on here, I have suffered greatly from the "manifold" rejections.
However, I seem to be seeing some light on this at long last, and while not comprehensive, or fully conclusive, here are the steps I have been taking which seem to produce results.
Create object in Rhino until happy with design.
Convert to mesh and show edges.
Use the Rhino tools to fill holes, join naked edges.
Save as an STL.
Thanks to other threads on this forum, I have downloaded MiniMagics and MeshLab.
I look at the STL file with MiniMagics and it shows lots of errors. It is a viewer only so only good as a diagnostic tool.
I then load the STL into MeshLab and Close Holes, Remove Unreferenced Vertex, Remove Zero Area Face, Remove Non Manifold Faces.
I save the file.
Back into Rhino with a new, blank, model and import the STL. Check edges and there are new ones which never existed before. Fill holes, join naked edges again and resave as an STL. I do not bother saving as a Rhino file at this stage.
Back into MeshLab and Remove Non Manifold Faces, some have usually turned up although we got rid of hem the first time.
Save the STL.
Check with MiniMagics and it should be ok and ready to upload the Shapeways.
These are not definitive instructions, but I have followed this method several times now and it has worked. I hope it will help someone.
Feel free to correct me if I have managed to get some of this in the wrong order, or have missed something.