GameDaily seems confident that Neversoft will take over the franchise beginning with Guitar Hero III, but this is only one possibility. Other current Guitar Hero rumors (again, perpetuating from EGM) include an 80's version of the series to see release this year, which Neversoft could be working on, leaving the brand name sequels to Harmonix.
And where does this leave Harmonix? While one would assume they'll still be involved with the series, they could very well be off starting up a new franchise, or perhaps working on one of those rumored Amplitude sequels. Regardless, they've laid out the foundation for an extremely popular and established series. Hopefully this changing of the guard will be more like a Sammy Hagar and less like a Gary Cherone.