When you run configure --with-dom it only checks that you have the libxml library >= 2.2.7. However the libxml 2.3.x series doesn't work with PHP and causes undefined symbols (Either during linking or when Apache loads the module)

I used the following configure options:
./configure  --with-apxs=/usr/apache/bin/apxs --with-zlib --with-regex=system --with-readline --with-pdflib --with-mysql=/home/mysql --with-gettext --enable-ftp --with-gd=../gd-1.8.4 --with-bz2 --enable-calendar --with-dom --with-java=/usr/local/jdk1.3

Here is a simplistic patch that does a poor job of checking that the 2.3.x series is not in use.

*** ext/domxml/config.m4.orig	Wed Mar  7 22:56:54 2001
--- ext/domxml/config.m4	Wed Mar  7 23:00:36 2001
***************
*** 4,19 ****
  AC_DEFUN(PHP_DOM_CHECK_VERSION,[
    old_CPPFLAGS=$CPPFLAGS
    CPPFLAGS="-I$DOMXML_DIR/include"
!   AC_MSG_CHECKING(for libxml version)
    AC_EGREP_CPP(yes,[
    #include <libxml/xmlversion.h>
    #if LIBXML_VERSION >= 20207
    yes
    #endif
    ],[
!     AC_MSG_RESULT(>= 2.2.7)
    ],[
!     AC_MSG_ERROR(libxml version 2.2.7 or greater required.)
    ])
    CPPFLAGS=$old_CPPFLAGS
  ])
--- 4,21 ----
  AC_DEFUN(PHP_DOM_CHECK_VERSION,[
    old_CPPFLAGS=$CPPFLAGS
    CPPFLAGS="-I$DOMXML_DIR/include"
!   AC_MSG_CHECKING([for libxml - version >= 2.2.7, < 2.3.x])
    AC_EGREP_CPP(yes,[
    #include <libxml/xmlversion.h>
    #if LIBXML_VERSION >= 20207
+   #if LIBXML_VERSION < 20300
    yes
    #endif
+   #endif
    ],[
!     AC_MSG_RESULT(yes)
    ],[
!     AC_MSG_ERROR([libxml version 2.2.7 or greater (but not 2.3.x series) required.])
    ])
    CPPFLAGS=$old_CPPFLAGS
  ])