The "killer apps" for Linux have never been GNU. Apache httpd and XFree86/Xorg are by far and above the most popular applications on Linux, and they aren't GNU projects.
Graphically, GNU is at its nadir of influence. Freedesktop.org controls most cross-desktop standards, libraries, and services. GNU's own desktop environment GNOME is no longer nearly as popular as it used to be thanks to GNOME 3 being actively hostile to desktop users (and GNOME has always been part of GNU on paper only -- it's effectively a Red Hat project).
On the platform side, the init system has never been GNU. While the init system has always been a minor part of the OS, this is changing thanks to systemd (also a product of freedesktop.org) getting its hooks into everything on several levels.
Actually, I'd go as far as to say that freedesktop.org has far more influence on the userland than GNU does right now.