There are almost no differences. The details of the differences can be found in the 2009 New Car Features manual. You can download this for a nominal $10 fee which includes a day's unlimited downloading from
http://techinfo.toyota.com/ Besides the 2009 NCF manual you can also download the 2004 NCF manual which has over 50 chapters about how the Prius works (and it's in an understandable format). The NCF manual is much more informative than the owners manual.
It still may be possible to get a brand new 2009. There won't be any brand new 2008s.