My configuration:

./configure  --with-apache=../apache-1.3.9
--with-ftp --with-mysql=shared,/opt/mysql --enable-track-vars
--with-config-file-path=/etc --with-gd=shared,../gd-1.3 --with-freetype
--with-imap=/usr/src/imap/c-client --with-mm --with-pdflib=../pdflib-2.01
--enable-thread-safety --with-tiff-dir=/usr/lib --with-jpeg-dir=/usr/lib
--enable-trans-sid --enable-sysvshm --enable-sysvsem
--with-xml=shared,../apache-1.3.9/src/lib/expat-lite/

root@gateway:/usr/src/www/php4/ext/gd
# make
/bin/sh ../../libtool --silent --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I../.
. -I../../libzend -I../../TSRM -I/usr/src/www/php4/../apache-1.3.9/src/include -
I/usr/src/www/php4/../apache-1.3.9/src/os/unix   -I/usr/src/imap/c-client/includ
e   -I/usr/local/include  -I/usr/include -I../gd-1.3 -I../.. -I../../libzend
-g -O2 -g -O2 -c gd.c
In file included from gd.c:36:
php3_gd.h:49: gd.h: No such file or directory
gd.c:50: gd.h: No such file or directory
gd.c:51: gdfontt.h: No such file or directory
gd.c:52: gdfonts.h: No such file or directory
gd.c:53: gdfontmb.h: No such file or directory
gd.c:54: gdfontl.h: No such file or directory
gd.c:55: gdfontg.h: No such file or directory
make: *** [gd.lo] Error 1

Editing the Makefile and changing -I../gd-1.3 to -I../../../gd-1.3 fixes the problem.