libtool doesn't pass library options (-l, -L) to the compiler when linking the final library;
I use the following flags to configure PHP4:
--with-regex=system --without-gd --with-zlib
--with-yp --with-filepro
--with-config-file-path=${PREFIX}/etc
--with-exec-dir=${PREFIX}/libexec/php3 
--enable-track-vars --enable-force-cgi-redirect
--enable-discard-path --enable-memory-limit
--disable-pear --disable-debug --disable-rpath
--with-apxs=${LOCALBASE}/sbin/apxs
--with-pgsql=${LOCALBASE}/pgsql
(LOCALBASE and PREFIX environment variables are set)

Here is the output of libtool (I removed --silent option):
cc -shared  -Wl,--rpath -Wl,/usr/pkgsrc/www/php4-apache/work/php-4.0b4pl1/libs  
main.lo internal_functions.lo snprintf.lo php_sprintf.lo configuration-parser.lo
 configuration-scanner.lo safe_mode.lo fopen-wrappers.lo php_realpath.lo alloca.
lo php_ini.lo SAPI.lo rfc1867.lo dlist.lo php_content_types.lo strlcpy.lo strlca
t.lo mergesort.lo reentrancy.lo php_variables.lo -Wl,--whole-archive Zend/.libs/
libZend.al sapi/apache/.libs/libsapi.al ext/db/.libs/libdb.al ext/filepro/.libs/
libfilepro.al ext/pcre/.libs/libpcre.al ext/pgsql/.libs/libpgsql.al ext/posix/.l
ibs/libposix.al ext/session/.libs/libsession.al ext/standard/.libs/libstandard.a
l ext/yp/.libs/libyp.al ext/zlib/.libs/libzlib.al -Wl,--no-whole-archive -Wl,-soname -Wl,libphp4.so.0 -o .libs/libphp4.so.0.0