One of the arguments that I hear from people who want to emphasize the advantage of web applications is usually that you can access your application and data (e.g. webmail) from every computer.
But think of it: What are the PCs you really trust? For me it is a very few not more than 3 or 4. When I am at a customer or at a friend or somewhere else - the only PC that I really trust is the one that I bring along.
And thinking of GTD, on a different PC you will not have your keyboard shortcuts configured and other options set that allow you to be efficient. You can't really be highly productive without having setup your personal environment with the tools, settings and shortcuts that give you a boost. Being on a foreign PC sometimes my problems already start when grabbing the mouse as many may have different mouse acceleration settings than me.
Using a USB stick with your portable applications installed and configured is not a real solution as it binds you to a particular OS to be found at the client at least.
So it really makes sense to take your machine with you. With the rise of netbooks it even got easier to carry your machine with you. And you will have it configured to make you most productive and efficient.
Related posts: Web vs Thick client, The mobile device, Web application security, Pros and cons of cloud solutions, User lock down.