User Interface Engineering (UIE) have released a 54 page report called The Designer’s Guide to Web Applications, Part I – Structure and Flows . It’s US$35 – but there’s a free chapter available for download.
I’ve read the free chapter, and it’s very good. It helps conceptualise how most web applications should be structured – useful if you’re struggling to envisage how screens should ‘flow’ from one to the other.
In a similar vein, there is Bob Baxley‘s Task Flow for Web Applications, part 1 – Views & Forms and Task Flow for Web Applications, part 2 – Wizards & Guides.