Patterns and Practices team just released version 2 of the Web Client Software Factory. Among new features are implementation of MVP pattern for user controls and master pages, and a few AJAX extender controls.
PageFlow is not present in this release, and its future seems to be murky. I spent some time trying to implement PageFlow in my project and was disappointed by its complexity. Benefit to effort ratio was definitely too low; I eventually gave up on it.
I have followed the steps outlined in documentation in order to migrate my solution from June 2007 (1.1) release of the factory without much trouble. Unfortunately, there is still no recipe to add new website to the solution. So, if you need to have more than one, make a copy of the existing website and add it. Make sure little file called vwd.webinfo is present in the root of the website, otherwise WCSF will not "recognize" it - new site name will not appear in drop-down lists or will be grayed out when you execute various recipes from the guidance package. I don't believe this tip is documented.