I am still using GATK1.6 version, and I am thinking to buy an new version GATK 2.8 now. However, I would like to know any major differences between old and new version.
We provide release notes documenting changes for each version, which you're welcome to look through here: http://www.broadinstitute.org/gatk/guide/version-history
If you're looking for a detailed comparison between 1.6 and 2.8 specifically, I would refer you to our commercial partner, Appistry. They will be able to give you a breakdown of the value proposition for the commercial GATK license and 2.8 features.