I just recently installed a JBL sound system (amp and speakers) from a junkyard Camry ($50 for the whole lot) and am VERY impressed with the improvement in sound quality over the stock system, still using the stock head unit.
Regarding aftermarket speakers and amp(s), "best" is a very flexible term because it will all depend on how much you are willing to spend. For instance, a dedicated subwoofer with its own power supply can make the whole rest of the system sound incredible simply because you can cut way down on how hard everything else has to work.
Regarding touch screen head units, name brands like Pioneer, Alpine and Kenwood are all well proven and have huge range of prices/options. There are also "no name" Chinese head units which cost far less, but come with their own menu of potential problems (they are sometimes rejected name brand parts sold from the scrap bin, its hard to know for sure).