This is an inherent problem with web apps, since they're an app within an app. There are two different contexts fighting each other. Who's to say that Ctrl+S should save the app state or the page? Whatever we choose as the default, the non-default scenario would feel awkward when we need it.
I can think of two ways to solve this: (1) decouple apps from the browser frame or (2) use a special modifier key for app shortcuts (perhaps re-use the Windows key, e.g. Win+Ctrl+S).
Yeah, that's pretty messy. As an Opera user I had no idea that other browsers used Ctrl or Alt for access keys. That's just a recipe for disaster. Opera's Shift+Esc combo guaranteed no clashes with browser shortcuts, but it was really kludgy to use.
I can think of two ways to solve this: (1) decouple apps from the browser frame or (2) use a special modifier key for app shortcuts (perhaps re-use the Windows key, e.g. Win+Ctrl+S).