So, from the top...
Nike originally the Free to be a shoe that would mimic barefoot running on grass.
And when running barefoot on a soft surface, people still tend to heel strike which is why the Nike Free shoes still have some cushioning under the heel.
The numbering system assumes 0.0 is barefoot and 10.0 is a regular running shoe.
The other number in the name is the version number of that shoe.
As of April 2012 we are up to:
Nike Free 3.0 V4 (version 4)
Nike Free 4.0 V2 (version 2)
Nike Free Run+ 2 (5.0) (version 2)
The Nike Free Run was always the most cushioned in the series and didn't previously have a *.0 number attributed to it. The first version I put at around a 6.0 or 7.0, but the new version 2 has 5.0 moulded onto its midsole. As mentioned above, the + in the shoe's name means it is the only one that can accomodate the Nike+ Speed & Distance chip.
Edited: 07/06/2012 at 00:52