I would love the "perfect" GTD software system, but I'm not sure there will ever be a single perfect app for everyone -- just look at all the different approaches taken by the posters on this board.
On the other hand, if such an app were ever written . . . I wouldn't want it to be a webapp. If my connection to the web went down, or I was out of touch somehow, I wouldn't want to lose access to my lists, etc.
Just one man's thoughts.