[eridius]

The problem with invisible updates is sometimes you don't want to get the update at all. This is especially true if you work in a corporate environment and you need to re-certify each version of the app for use on your work-provided devices.

[tlrobinson]

HTML5's Application Cache can solve that to some extent. I believe you can prompt to user to ask if they want to update (though once it's updated there's no going back, or installing previous version initially, unless the site provides mirrors of old version)

[saurik]

This question is only going to be relevant if the application is already open: if you close your browser windows and then re-open the application it will use the latest cache and evict the older ones. In essence, this mechanism is designed to allow an application to operate with an atomic version of the resources it requires for operation, and is not designed to allow the user to manage old versions.