Navigation. Since a web application runs in the browser, users expect to be able to use the browser's buttons for navigation, such as using the Back button to return to the previous page. However, handling this type of navigation correctly is tricky, so it's important to design an interface that encourages the user to use other means for navigation.
I think, that (1) either one uses document-based model native to a browser, and allow a user to click Back, Forward, Reload buttons and even to leave the page and return back using page URL; or (2) one uses window-based model and builds the UI using applets, web-start or Flash. There are a lot of websites around which look like normal web pages, but behave weird when one clicks Back or Reload. A user must
be allowed to click Back button, it is the application responsibility to return a proper response.
A web application is task-oriented, comprised of pages that must be entered in a specific sequence, rather than free-form set of links as in a traditional web site. Users must be allowed to jump directly to specific pages only, such as the main pages for different tasks.
Pages of web application usually do not have to be entered in a specific sequence, it is the pages of a wizard which has a sequence. And wizards usually take a relatively little portion of the whole application. Even if the whole application is a one big wizard, a user must
be allowed to jump wherever he wants, it is the application responsibility to track the state and to return a proper response.
Bookmarks. Bookmarking is related to navigation and can also be hard to support in a web application; you don't want a user to bookmark a page that should only be accessed as a result of submitting a form, for instance.
Which is why one should use redirection and never
display a result page as a direct response to form submission.
Although I dislike HTML frames on a regular web site, frames can be useful in web applications because they prevent users from bookmarking individual pages.
Goodbye, the concept of accesibility.