Most non-linear editors have the ability to slow sections. There just aren't that many good free ones to recommend however.
Lightworks can do this. Do a Google search for it and you'll find a tutorial or two.
This is a complex program.
Another free NLE that is often recommended is AviUtl. It was originally released in Japan, but there is an English version over at Videohelp.com: http://www.videohelp.com/software/AviUtl
Download the AviUtl Extra Pack version.
The problem with this program is that there aren't many people using it, and you won't find much help.
What you are trying to do is not something I have attempted. So I will be zero help. Ask over at Videohelp.com or Doom9.org.