But I wonder if you could use popup windows and/or frames, combined with JavaScript/DHTML for updating, to get the same effect you have in a desktop app where a new mode can be pushed onto the stack without touching the state of anything beneath

I would be leery of that. A great temptation with web apps is overdesign and non-standard behavior, and using frames with DHTML is just asking for trouble. You'll end up having to support ten versions of your code for different browser/OS configuratons.

One good idea is to spend some time on sites like Expedia, JetBlue, Amazon, Southwest Airlines and other web apps that have to maintain a lot of state and allow for users to do lateral navigation. Steal ideas from them, notice how they do error handling, UI design, and so on.

When that is done, mock up your HTML pages. Then write code using fictitious subroutines / objects / whatever you like, at as high a level of abstraction as you can. Once you are satisfied with the overall architecture, move down a level of abstraction, using stub objects / subroutines, and then move down another level, until finally you have coded the whole thing out.

Of course the process is never so pat and linear, but I've found it's a good model to work from. The most important part is looking at lots of other web applications, preferably ones run by companies that have poured money into usability testing.