Exactly what linux distro are you using? And does this work:

# rm -f config.cache ; ./configure --disable-all --disable-cgi && make

The linux version this is running on is RedHat Enterprise Linux.  I believe it's version 4. 
 
Running:
[root@les1 php5.3-200908110030]# rm -f config.cache ; ./configure --disable-all --disable-cgi && make

resulted in:

/bin/sh /home/automan/php5.3-200908110030/libtool --silent --preserve-dup-deps --mode=link gcc -export-dynamic -g -O2     ext/date/php_date.lo ext/date/lib/astro.lo ext/date/lib/dow.lo ext/date/lib/parse_date.lo ext/date/lib/parse_tz.lo ext/date/lib/timelib.lo ext/date/lib/tm2unixtime.lo ext/date/lib/unixtime2tm.lo ext/date/lib/parse_iso_intervals.lo ext/date/lib/interval.lo ext/ereg/ereg.lo ext/ereg/regex/regcomp.lo ext/ereg/regex/regexec.lo ext/ereg/regex/regerror.lo ext/ereg/regex/regfree.lo ext/pcre/pcrelib/pcre_chartables.lo ext/pcre/pcrelib/pcre_ucd.lo ext/pcre/pcrelib/pcre_compile.lo ext/pcre/pcrelib/pcre_config.lo ext/pcre/pcrelib/pcre_exec.lo ext/pcre/pcrelib/pcre_fullinfo.lo ext/pcre/pcrelib/pcre_get.lo ext/pcre/pcrelib/pcre_globals.lo ext/pcre/pcrelib/pcre_info.lo ext/pcre/pcrelib/pcre_maketables.lo ext/pcre/pcrelib/pcre_newline.lo ext/pcre/pcrelib/pcre_ord2utf8.lo ext/pcre/pcrelib/pcre_refcount.lo ext/pcre/pcrelib/pcre_study.lo ext/pcre/pcrelib/pcre_tables.lo ext/pcre/pcrelib/pcre_try_flipped.lo ext/pcre/pcrelib/pcre_valid_utf8.lo ext/pcre/pcrelib/pcre_version.lo ext/pcre/pcrelib/pcre_xclass.lo ext/pcre/php_pcre.lo ext/reflection/php_reflection.lo ext/spl/php_spl.lo ext/spl/spl_functions.lo ext/spl/spl_engine.lo ext/spl/spl_iterators.lo ext/spl/spl_array.lo ext/spl/spl_directory.lo ext/spl/spl_exceptions.lo ext/spl/spl_observer.lo ext/spl/spl_dllist.lo ext/spl/spl_heap.lo ext/spl/spl_fixedarray.lo ext/standard/crypt_freesec.lo ext/standard/crypt_blowfish.lo ext/standard/php_crypt_r.lo ext/standard/array.lo ext/standard/base64.lo ext/standard/basic_functions.lo ext/standard/browscap.lo ext/standard/crc32.lo ext/standard/crypt.lo ext/standard/cyr_convert.lo ext/standard/datetime.lo ext/standard/dir.lo ext/standard/dl.lo ext/standard/dns.lo ext/standard/exec.lo ext/standard/file.lo ext/standard/filestat.lo ext/standard/flock_compat.lo ext/standard/formatted_print.lo ext/standard/fsock.lo ext/standard/head.lo ext/standard/html.lo ext/standard/image.lo ext/standard/info.lo ext/standard/iptc.lo ext/standard/lcg.lo ext/standard/link.lo ext/standard/mail.lo ext/standard/math.lo ext/standard/md5.lo ext/standard/metaphone.lo ext/standard/microtime.lo ext/standard/pack.lo ext/standard/pageinfo.lo ext/standard/quot_print.lo ext/standard/rand.lo ext/standard/soundex.lo ext/standard/string.lo ext/standard/scanf.lo ext/standard/syslog.lo ext/standard/type.lo ext/standard/uniqid.lo ext/standard/url.lo ext/standard/var.lo ext/standard/versioning.lo ext/standard/assert.lo ext/standard/strnatcmp.lo ext/standard/levenshtein.lo ext/standard/incomplete_class.lo ext/standard/url_scanner_ex.lo ext/standard/ftp_fopen_wrapper.lo ext/standard/http_fopen_wrapper.lo ext/standard/php_fopen_wrapper.lo ext/standard/credits.lo ext/standard/css.lo ext/standard/var_unserializer.lo ext/standard/ftok.lo ext/standard/sha1.lo ext/standard/user_filters.lo ext/standard/uuencode.lo ext/standard/filters.lo ext/standard/proc_open.lo ext/standard/streamsfuncs.lo ext/standard/http.lo TSRM/TSRM.lo TSRM/tsrm_strtok_r.lo TSRM/tsrm_virtual_cwd.lo main/main.lo main/snprintf.lo main/spprintf.lo main/php_sprintf.lo main/safe_mode.lo main/fopen_wrappers.lo main/alloca.lo main/php_scandir.lo main/php_ini.lo main/SAPI.lo main/rfc1867.lo main/php_content_types.lo main/strlcpy.lo main/strlcat.lo main/mergesort.lo main/reentrancy.lo main/php_variables.lo main/php_ticks.lo main/network.lo main/php_open_temporary_file.lo main/php_logos.lo main/output.lo main/getopt.lo main/streams/streams.lo main/streams/cast.lo main/streams/memory.lo main/streams/filter.lo main/streams/plain_wrapper.lo main/streams/userspace.lo main/streams/transports.lo main/streams/xp_socket.lo main/streams/mmap.lo main/streams/glob_wrapper.lo Zend/zend_language_parser.lo Zend/zend_language_scanner.lo Zend/zend_ini_parser.lo Zend/zend_ini_scanner.lo Zend/zend_alloc.lo Zend/zend_compile.lo Zend/zend_constants.lo Zend/zend_dynamic_array.lo Zend/zend_execute_API.lo Zend/zend_highlight.lo Zend/zend_llist.lo Zend/zend_opcode.lo Zend/zend_operators.lo Zend/zend_ptr_stack.lo Zend/zend_stack.lo Zend/zend_variables.lo Zend/zend.lo Zend/zend_API.lo Zend/zend_extensions.lo Zend/zend_hash.lo Zend/zend_list.lo Zend/zend_indent.lo Zend/zend_builtin_functions.lo Zend/zend_sprintf.lo Zend/zend_ini.lo Zend/zend_qsort.lo Zend/zend_multibyte.lo Zend/zend_ts_hash.lo Zend/zend_stream.lo Zend/zend_iterators.lo Zend/zend_interfaces.lo Zend/zend_exceptions.lo Zend/zend_strtod.lo Zend/zend_gc.lo Zend/zend_closures.lo Zend/zend_float.lo Zend/zend_objects.lo Zend/zend_object_handlers.lo Zend/zend_objects_API.lo Zend/zend_default_classes.lo Zend/zend_execute.lo sapi/cli/php_cli.lo sapi/cli/php_cli_readline.lo main/internal_functions_cli.lo -lcrypt -lresolv -lcrypt -lm -ldl -lnsl -lcrypt -lcrypt  -o sapi/cli/php
ext/standard/.libs/basic_functions.o(.text+0x7c2): In function `zm_shutdown_basic':
/home/automan/php5.3-200908110030/ext/standard/basic_functions.c:3686: undefined reference to `zm_shutdown_crypt'
collect2: ld returned 1 exit status
make: *** [sapi/cli/php] Error 1

# make clean && make 

..and what compiler are you using? Version?

What's really irritating about this issue is that PHP has been successfully built on this machine in the past; as recently as last month.  

[automan@les1 ~]$ gcc -v
Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=i386-redhat-linux
Thread model: posix
gcc version 3.4.6 20060404 (Red Hat 3.4.6-11)

Can you try the PHP_5_2 snapshot also:

  http://snaps.php.net/php5.2-latest.tar.gz

And are you absolutely sure nothing has changed in your system..?
I suggest trying to recompile the last PHP version you were able to build before..

No feedback was provided for this bug for over a week, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".

Try just 
rm -f config.cache
and your old ./configure params
works for me

Please try using this snapshot:

  http://snaps.php.net/php5.3-latest.tar.gz
 
For Windows:

  http://windows.php.net/snapshots/

Still got the same problem with last snapshot:

php5.3-201009010830/main/streams/glob_wrapper.c:40: error: expected specifier-qualifier-list before 'glob_t'

Red Hat Enterprise Linux Server release 5.4 (Tikanga)
gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)

This bug has been fixed in SVN.

Snapshots of the sources are packaged every three hours; this change
will be in the next snapshot. You can grab the snapshot at
http://snaps.php.net/.
 
Thank you for the report, and for helping us make PHP better.