The OS could be more intelligent about this if apps were classified according to what kind of application it is. An example: some apps on Mac OS X (Pages, Word, Browsers, etc.) doesn't do anything unless you have a document window open. If I haven't been using one for a while, a "document" application could just as well be closed. (In Windows/Linux it kinda works like this already though).
You'd have to find out what classes of applications you need, specify desired behaviour and perhaps create an API for them though, which is exactly what Apple has done with iOS. Personally I think it works quite well, for instance audio player applications work exactly as I would expect (works with media keys, doesn't compete for audio with other media apps, quits when I'm not using it anymore).
In a real desktop OS you'd obviously need to allow traditional management of apps though, but an unexperienced user shouldn't be required to use it.
Windows, Linux and Mac do this to some degree already I guess (especially for system services.. think xinetd and launchd), but I think it could be done better and more systematically. But then again.. everything could be done better or differently, so I'm not complaining. But it's not unreasonable to discuss how things might be better is it?