i'm not sure i understand your question. going to ipv6 is not really a choice you (an idividual) can make. if it is, its not a choice you can make yet. nothing has switched over to v6 yet. its still in the infancy of planning.

most likely wont be implemeneted for another couple of years at the earliest.

as for programs working, it depends on what programs, and in what fashion the programs were written... but its most likely that some things will need a re-write/update.

i'm sure others will be able to provide you with more info on it. i researched it last year, but forgot most of it already, lol.