I've been thinking a lot about the Windows Registry (and /etc, etc) and I've come to the conclusion that the systems which get it the most "right" is the app model (e.g. Android, iOS, Windows 8).
You see systems like Docker containers, which try to isolate a complete application and its configuration files together, and really that is just a hacky solution to the lack of inherent silo-ing within the underlying design.
While silo-ed apps have their own limitations (e.g. two "apps" using the same configurations) most of them can be overcome with tinkering for the edge cases.
I'd never design a system in 2014 with either Windows Registry (too messy, impossible to manage), or /etc (too inconsistent with itself, also often results in orphan files).
You see systems like Docker containers, which try to isolate a complete application and its configuration files together, and really that is just a hacky solution to the lack of inherent silo-ing within the underlying design.
While silo-ed apps have their own limitations (e.g. two "apps" using the same configurations) most of them can be overcome with tinkering for the edge cases.
I'd never design a system in 2014 with either Windows Registry (too messy, impossible to manage), or /etc (too inconsistent with itself, also often results in orphan files).