07+ models have more trim levels, Shelby, GT500, Bullitt.
07+ models have a different computer which requires a different tuner (if you go with a diablosport) and in some supercharger packages an install kit for them.
07+ models have also more chassis stiffening then the 05-06 models.
07+ models have a better and simpler designed routing for the cooling system.
07+ models come with a TPMS system.
07+ models are usually more expensive.
latter 08-09 models should have the redesigned cylinder head with the more traditional one piece spark plugs which don't fail when you try to remove them.
Starting to sound like the commandments here.
That's all I can think of for now.