configure.ac

AC_INIT([test1], [1.0])
AC_CONFIG_AUX_DIR(autoconf)
AC_CONFIG_MACRO_DIR(autoconf)
AM_INIT_AUTOMAKE([foreign subdir-objects]) 
AC_CONFIG_SRCDIR([configure.ac])
AC_PROG_CC
AC_CONFIG_FILES([Makefile])

AC_ARG_WITH([foo],
            [AS_HELP_STRING([--with-foo],
                            [enable foo (default=no)])],
            [enable_foo=$withval],
            [enable_foo=no])

AM_CONDITIONAL([ENABLE_FOO],[test x$enable_foo = xyes])

AC_OUTPUT

Makefile.am

if ENABLE_FOO
include $(srcdir)/Makefile.foo.include
endif

Makefile.foo.include

bin_PROGRAMS = test1

test1_SOURCES = test1.c

test1.c

#include <stdio.h>

int main()
{
        printf("Hello, world!\n");
        return 0;
}