My own "distro": https://github.com/ainriver/tonic
Its a messy pile of rules tho, but easy to hack some more stuff in or just generate a quick rootfs.
Beside from that, i remember the syslinux bootloader being that way. The linux kernel, busybox and the buildroot distribution also use kconfig, which is Makefile with some config engine in C. If you maintain packages for a distributions, you see what other stuff is used instead of autotools.
Do you have examples of non trivial projects that use only Makefiles and nothing else as a build system?