The thing I love about web apps is not having to worry about an installation dialog where I must be on the lookout for the program trying to place icons on my desktop, start menu, or elsewhere.
Seriously though, I understand developers react to someone changing a setting on their computer like a dragon who had a copper piece fondled by an unwelcome hobbit. However, normal people don't care, need those boxes checked or they will be unable to run the software again, and everything in an installer might as well be magic spells written in ancient Aramaic (though the cleverer ones have learned that the button on the bottom right casts "continue").
All I can think of now is "our website was at the very tip of the penis" and "my salesforce.com was on the right testicle". http://www.youtube.com/watch?v=W8_Kfjo3VjU
Bringing back a lightweight notion of installation offers an interesting way out of these constraints. If an author uses APIs like window.open() and desktop notifications in an annoying way, his app will be uninstalled. The UA can make it easy for the user to discover the uninstall button, so there's a strong incentive for authors to not be assholes.
The author has more confidence in the ability of regular users to identify the cause of a novel behavior on their computer than I do. For example, I sell downloadable software. My users largely understand that downloadable software is dangerous and Google is safe. When Google went down last year, three people did the following math: "Google was up, I installed Patrick's software, Google went down, clearly Patrick has broken the Google and needs to give it back or I will tell my husband."