Previously, I've complained about the U3D file format for having such an obscure encoding scheme that I felt it was impossible to read a U3D file without using the unreleased Intel U3D libraries that everyone else apparently uses to read and write this file format.
But after looking at some other 3d file formats, perhaps this isn't so unusual. For example, Kaydara's FBX file interchange format (now owned by Alias) doesn't even have a documented encoding format. As far as I can tell, the only way to read a FBX file is to use the provided SDK libraries. Personally, I can't imagine how you could call something an interchange file format if you don't actually describe what the file format is. But maybe I'm just not used to how things work with 3d graphics.
Oddly enough, the only light-weight 3d file format that seems to be well-documented is Microsoft's DirectX file format. Unfortunately, it's apparently no longer under active development.