There is a great summary article that reviews the various versions with changes in each version described and referenced.
Length of booster core
Here's an image showing the two Falcons side-by-side:
As you can see, Falcon 9 1.1 is much longer than its predecessor, Falcon 9 Block 1 had a liftoff height of 53 meters, versus Falcon 9 1.1's 69.2 meters. The stretch is to accommodate the additional fuel and oxidizer needed for the new more powerful engine.
Engine in use
The engine was changed from the Merlin 1-C to the Merlin 1-D which has higher thrust at 145,000 lbs at sea level. It is also reputed to be more easily manufactured.
The engine layout has changed. It changed from a 3X3 grid (tic tac toe) layout to the Octo-web layout of eight engines in a cirle, with a ninth in the center.
With the Jul 2013 update of the SpaceX web site, the Falcon 9 v1.1 has been pictured with landing legs. This is for the Reusable part of the F-9R moniker. Tweets from Elon Musk have suggested that they will also act as aerodynamic surfaces of some kind during descent.
Here's some more statistics in chart-ish form, from near the bottom of this page: