To be fair, there was no shortage of apps (especially in Win9x era) that did ignore system colors. Which actually took some effort to do, and almost invariably the result would be a gaudy eyesore, but the "it's branding!" people were already around, albeit not as prevalent.

Anyway, the last version of Windows that still maintained this functionality (in "Classic" theme) was Win7; Win8 no longer had the ability to disable Aero.