What I would like to see is a "privileged mode" Chromium (or Firefox) that would let applications break out of the browser sandbox and directly perform operations such as filesystem I/O. Privileged Mode Chromium would obviously be a huge security threat if it's allowed to run any old code, so it would be wise to prevent it from downloading and executing scripts over the network, or maybe have some kind of script signing support in place so that the only scripts allowed to execute are the ones with the app developers' signature on them. Or maybe I'm talking out of my ass here and what we have right now works just fine. Feel free to correct me here.
Also, one question. Isn't the node.js instance serving my application visible to other applications on the same system? Can't a malicious application take advantage of this fact and cause my app to misbehave?
(Offtopic: I must point out an irritating and potentially harmful design trend that is emerging as a result of Twitter Bootstrap's popularity: the top navigation bar that stays in place as you scroll downward. It wastes precious screen space, looks ugly and doesn't add anything of value to the website. Why is it so important that I be forced to look at your website's logo and navigation bar all the time? I'm not picking on the AppJS developers here; this is a general sentiment directed towards all the designers who embrace this terrible trend.)