Your question would require quite a long answer. General specs of the different formats, you can find many places online. Usually the files needed will contain the geometry and additional colour & texture files. (For transparency in .obj format, you could test different renderings with a combination of transparent graphic file and transparency in the .mtl file - see this thread and this thread).
As for the SH3D specifics you may want to have a look at the FurnitureLibraryEditor (see download page) which will allow you to supply additional model information.
For instance: .obj (and other import) files do not support some more advanced features like window/door cut-out, but this can be added with the FurnitureLibraryEditor. If you need light sources in the model and other advanced properties, you may just need to dive a little deeper into the file specifications (see Sourceforge docs).
An SVG mini-manual - specially from page 9 on - may possibly also give you a hint or two on how to add extra (SH3D specific) qualities to your models.
As for the camera / light you use in your 3D modelling software to produce a rendering, I guess you will need to substitute with light sources and view angles in SH3D - or am I misunderstanding what you are trying to do?
Best modelling software? What you feel most comfortable with
Blender is very good software once you get used to it. Art of Illusion or Sketchup are simpler... ok
PS I am curious as to how you use Inkscape for your 3D modelling. Sometimes it could be useful to start a model based on a 2D SVG sketch.
