I'm using gcc 2.7.2.2 on Solaris 2.6, and found that libtool will strip all -R directories from the input which leads to unresolved library links, see the following compiler output (removed --silent from $LIBTOOL command)

/bin/sh /local/tmp/php-4.0.2/libtool --mode=link gcc  -I. -I/local/tmp/php-4.0.2/ -I/local/tmp/php-4.0.2 -I/local/tmp/php-4.0.2/main -I/local/netscape/include -I/local/tmp/php-4.0.2/Zend -I/local/tmp/php-4.0.2 -I/local/gnu/include -I/local/mysql/include -I/local/ora816/rdbms/public -I/local/ora816/rdbms/demo -I/local/ora816/network/public -I/local/tmp/php-4.0.2/ext/xml/expat/xmltok -I/local/tmp/php-4.0.2/ext/xml/expat/xmlparse -I/local/tmp/php-4.0.2/TSRM  -D_POSIX_PTHREAD_SEMANTICS -D_POSIX_PTHREAD_SEMANTICS -D_REENTRANT -DXML_BYTE_ORDER=21 -I../TSRM -g -O2   -o libphp4.la -rpath /local/tmp/php-4.0.2/libs -avoid-version -L/usr/gnu/sun4-56/lib/gcc-lib/sparc-sun-solaris2.6/2.7.2.2 -L/local/gnu/lib -L/local/mysql/lib -L/local/ora816/lib  -R /usr/gnu/sun4-56/lib/gcc-lib/sparc-sun-solaris2.6/2.7.2.2 -R /local/gnu/lib -R /local/mysql/lib -R /local/ora816/lib stub.lo  Zend/libZend.la  sapi/nsapi/libsapi.la  main/libmain.la  regex/libregex.la  ext/db/libdb.la ext/dba/libdba.la ext/ftp/libftp.la ext/mysql/libmysql.la ext/oci8/liboci8.la ext/oracle/liboracle.la ext/pcre/libpcre.la ext/posix/libposix.la ext/session/libsession.la ext/standard/libstandard.la ext/xml/libxml.la ext/zlib/libzlib.la  TSRM/libtsrm.la -lgdbm -lpam -lstdc++ -lg++ -ldl -lz -lclntsh -lsched -ldl -lgen -lsocket -lnsl -lclntsh -lsched -ldl -lgen -lsocket -lnsl -lmysqlclient -lgdbm -lresolv -lresolv -lm -ldl -lcrypt -lnsl -lsocket -lpthread -lsocket -lgcc
rm -fr .libs/libphp4.la .libs/libphp4.* .libs/libphp4.*
/usr/ccs/bin/ld -G -h libphp4.so -o .libs/libphp4.so  stub.lo -z allextract Zend/.libs/libZend.al sapi/nsapi/.libs/libsapi.al main/.libs/libmain.al regex/.libs/libregex.al ext/db/.libs/libdb.al ext/dba/.libs/libdba.al ext/ftp/.libs/libftp.al ext/mysql/.libs/libmysql.al ext/oci8/.libs/liboci8.al ext/oracle/.libs/liboracle.al ext/pcre/.libs/libpcre.al ext/posix/.libs/libposix.al ext/session/.libs/libsession.al ext/standard/.libs/libstandard.al ext/xml/.libs/libxml.al ext/zlib/.libs/libzlib.al TSRM/.libs/libtsrm.al -z defaultextract  -L/usr/gnu/sun4-56/lib/gcc-lib/sparc-sun-solaris2.6/2.7.2.2 -L/local/gnu/lib -L/local/mysql/lib -L/local/ora816/lib -lgdbm -lpam -lstdc++ -lg++ -ldl -lz -lclntsh -lsched -ldl -lgen -lsocket -lnsl -lmysqlclient -lgdbm -lresolv -lresolv -lm -ldl -lcrypt -lnsl -lsocket -lpthread -lsocket -lgdbm -lpam -lstdc++ -lg++ -ldl -lz -lclntsh -lsched -ldl -lgen -lsocket -lnsl -lclntsh -lsched -ldl -lgen -lsocket -lnsl -lmysqlclient -lgdbm -lresolv -lresolv -lm -ldl -lcrypt -lnsl -lsocket -lpthread -lsocket -lgcc -lc 
creating libphp4.la
(cd .libs && rm -f libphp4.la && ln -s ../libphp4.la libphp4.la)

This is not really a bug in php, but an issue with libtool. It is possilbe to hard-code library-paths into shared libraries with the latest development release (1.3d) of libtool.