@swaiba -- I have to respectfully disagree with you... I think one of the biggest limitations of the framework right now is that "mysite" just becomes a huge dumping ground for all kinds of disparate code. Smaller, bite-sized modules would really help keep things organized.
@Willr -- Two comments..
1) I read about the "Developer mailing list" yesterday in the docs, but the link took me to an empty wiki page. Do you have the info? I'm interested.
2) If I can share my thoughts on the folder structure, I like most of it as it is, and I don't think too much has to be changed. The only thing that bothers me right now is that sapphire is at the same level as cms, mysite, and all the other modules. I would like to see Silverstripe evolve into more of a framework-based solution, and emulate the design patterns seen in frameworks like Symfony or Zend. It would be great if the sapphire framework lived external to, or above, all of the working files that we use in module directories. I'd also like to see CMS treated like a module, since, in an ideal world, it's an independent application built on the Sapphire framework. I understand they're pretty tied together right now, but I'd like to see a day where there was a bit more autonomy between the two.
In general, a progression toward more modules and less of a catch-all mysite folder is a good one. If you've ever built a site with 50+ templates you'll see why. It's easy to organize the code folder, but templates can't have subdirectories, and it just gets nasty. I think it would be wise to think of individual page types, their models, controllers, templates, CSS/JS dependencies, as individual modules.
This is a good thread. I'm glad someone brought this up!