To create 3D PDFs with software from Adobe, you pay $699 for Acrobat 9 Pro Extended. Or, $95 from QuadriSpace. I'll let QuadriSpace prez Brian Roberts explain the difference:
Unlike Acrobat Professional Extended, which merely allows users to add 3D to existing PDF documents, QuadriSpace's patented approach allows users to author documents from scratch and share these as 3D PDF documents complete with text, tables, multiple pages, markups and clickable bookmarks that animate between 3D views.
In addition, Acrobat requires the use of an external program to edit the 3D; QuadriSpace provides an integrated environment that lets users edit the 3D directly without leaving the document authoring application.
The QuadriSpace Personal Edition is free, downloadable from here (after providing personal information). The 3D PDF function is an extra $95.