In June 1991 I was maintaining many of the GNU utilities for the Free Software Foundation. As they were ported to more platforms and more programs were added, the number of -D options that users had to select in the makefile (around 20) became burdensome. Especially for me—I had to test each new release on a bunch of different systems. So I wrote a little shell script to guess some of the correct settings for the fileutils package, and released it as part of fileutils 2.0. That configure script worked well enough that the next month I adapted it (by hand) to create similar configure scripts for several other GNU utilities packages. Brian Berliner also adapted one of my scripts for his CVS revision control system.
Later that summer, I learned that Richard Stallman and Richard Pixley were developing similar scripts to use in the GNU compiler tools; so I adapted my configure scripts to support their evolving interface: using the file name Makefile.in as the templates; adding `+srcdir', the first option (of many); and creating config.status files.