I like .3ds because glass material & smooth object properties are work fine. And I like .obj because of its editable material file & most common 3D application support.
With the free version of Sketchup, your options are limited to Collada (.dae) - a tidy xml format (Sketchup .kmz export is just a compressed file with a .dae file + extra geo information in the .kml file). I have never had any problems with Sketchup's .dae export in SH3D, so I think I'd stick with the "default" Collada (.dae). Even if, in general, I prefer the clean, compact format of the .obj files... ok
Meanwhile I am using .dae (creating models using SketchUp Make = free version) which works fine. Also importing .dae files into SH3D works like a charm