After updating autoconf to 2.52 I've noticed that php is 
working with this autoconf version yet.

Even 'autoupdate' didn't helped to fix it.

I've taken a look at the generated shell code and noticed 
that some 'if-then-else' had an empty else-tree (else fi) 
which caused several unexpected shell exits. 
  These empty else-trees were the result of the following 
commands:
  AC_CHECK_FUNC(yp_get_default_domain,
 [php_no_nsl_checks=yes],[ ])
                         ^^^

That [ ] is the problem. If it is replaced by [] the else 
tree won't be build.

This applies to nearly all macros. The only exception is 
AC_DEFINE which requires a [ ] as third parameter if it is 
set at all.

Another issue was the PHP_SUBST in the acinclude.m4. I 
don't know what the five PHP_SUBST are doing there, but 
they will have to go into the configure.in the satisfy 
autoconf.

(acinclude.m4:930 [somewhere there])

PHP_SUBST(EXT_SUBDIRS)
PHP_SUBST(EXT_STATIC)
PHP_SUBST(EXT_SHARED)
PHP_SUBST(EXT_LIBS)
PHP_SUBST(EXT_LTLIBS)

I've uploaded the corresponding patch to 
http://jan.kneschke.de/projects/phpbugs/php4-20010821.diff

The patch is just a proof of concepts and doesn't fix 
every glitches, but it provides an working example.