Pretty much any Vector drawing program can be used to do this, like Freehand, or Illustrator. It doesn't have to be a program just like Visio.

Have you checked out OpenOffice.org? Draw, which is included with OpenOffice.org, will do just that, though it doesn't have as many features as Visio. It will let you do a rudimentary (or not so rudimentary, if you put the time in) yes/no diagram, like you're asking for.