Here is an example of a hack to get a web application to behave like a native application. Writely has inline spell checking. However, in firefox when you right click on the misspelled word, their are two menus that show up. The first one is the browsers right-click menu, and the second is googledocs own right click menu.
This is a good example that shows the short comings of current web applications. Web applications will always remain second to native applications as long as these issues remain. I have no problems with that myself, I prefer native applications. I want to be able to buy software, and own it. I want data to be on my machines. The world is moving away from that though.