This feature was mentioned a couple of times before. In code, you can simply instantiate any nodes you want, you can add them as a children of other nodes, you can set their fields as you like, and so on. Also several methods for enumerating and searching the nodes graph are provided (like EnumerateNodes and FindNode). See units reference for details.

I made a decent converter from 3DS, Wavefront OBJ and other file formats to X3D this way. Once I was able to read these files, it was trivial to construct according VRML/X3D graphs for them. You can then save constructed VRML/X3D graph to a file (so user can actually use this converter) and you can further process and render them just like any other VRML nodes graph (so my engine seamlessly handles 3DS and Wavefront files too, even though it's almost solely oriented on VRML).

This also allows authors to include 3DS, Wavefront OBJ and other files inside VRML/X3D files by Inline nodes, making it possible to create scenes in mixed 3D formats.