Hi, I am not sure if I understand your question. If QV has to save anything like Bookmarks or other settings it uses the Registry and saves files here : C:\Users\<user>\AppData\Roaming\QlikTech\QlikView , on Windows 7. You will find similar on XP in Documents and settings.
The ajax client does not store any files on your computer, except some static files (html, js, images...) that are cached by the browser (hence the name "zero footprint client"). Objects created with the ajax client are stored on the server in the documents folder.
I don't know if there is file stored on the client machine when the plugin is used to access server documents.