In the Planet Construction Kit, I introduced some 3-D modeling programs, but that section is pretty outdated. What I recommend now (if you can’t afford a pro package) is Blender, which is free and full of features. But like every other 3-D program, it’s complex and baffling and you can’t really figure it out just by messing with it. So, I wrote a tutorial that gives the basics of Blender.
It isn’t a full manual… that’d be a book in itself… but you can get pretty far with it. If people like it, I could add more (I only barely cover UV maps and creating humanoids).