Here is the gdb log:

[root@floyd bin]# gdb php
GNU gdb Red Hat Linux (5.3.90-0.20030710.41rh)
Copyright 2003 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "i386-redhat-linux-gnu"...Using host libthread_db library "/lib/tls/libthread_db.so.1".

(gdb) run -v
Starting program: /usr/local/bin/php -v
[Thread debugging using libthread_db enabled]
[New Thread -1084790912 (LWP 16385)]
PHP 5.0.0 (cli) (built: Jul 20 2004 11:59:59)
Copyright (c) 1997-2004 The PHP Group
Zend Engine v2.0.0, Copyright (c) 1998-2004 Zend Technologies
with Xdebug v2.0.0dev, Copyright (c) 2002, 2003, 2004, by Derick Rethans

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1084790912 (LWP 16385)]
0x007612f2 in _int_free () from /lib/tls/libc.so.6
(gdb) bt
#0 0x007612f2 in _int_free () from /lib/tls/libc.so.6
#1 0x0076028b in free () from /lib/tls/libc.so.6
0000002 0x001e2005 in zm_post_zend_deactivate_xdebug ()
at /home/maciek/nowe/xdebug2/xdebug/xdebug.c:566
0000003 0x08206796 in exec_done_cb (module=0x94f98)
at /home/maciek/nowe/php-5.0.0/Zend/zend.c:834
0000004 0x0820c365 in zend_hash_apply (ht=0x1f1fad,
apply_func=0x8206780 <exec_done_cb>)
at /home/maciek/nowe/php-5.0.0/Zend/zend_hash.c:664
0000005 0x082067bd in zend_post_deactivate_modules ()
at /home/maciek/nowe/php-5.0.0/Zend/zend.c:842
0000006 0x081d46be in php_request_shutdown (dummy=0x0)
at /home/maciek/nowe/php-5.0.0/main/main.c:1215
0000007 0x08232c93 in main (argc=2, argv=0xbfe8db84)
at /home/maciek/nowe/php-5.0.0/sapi/cli/php_cli.c:1046
(gdb)

Valgrind output:

==27885== Invalid free() / delete / delete[]
==27885== at 0x3C01F918: free (vg_replace_malloc.c:127)
==27885== by 0x3C88B4CB: zm_post_zend_deactivate_xdebug (xdebug.c:566)
==27885== by 0x82D7033: exec_done_cb (zend.c:834)
==27885== by 0x82DF86D: zend_hash_apply (zend_hash.c:664)
==27885== Address 0x3C89E67E is not stack'd, malloc'd or free'd

(If you want a workaround, just comment out that line 566 and it should work).

Actually, setting "xdebug.idekey" to anything makes a better solution.
(this option is not documented)

Seems that there should be more care taken of "ide_key" variable in the code.

This is fixed in CVS now, we had a problem where we used two different styles of memory allocation functions.
The idekey setting is now also documented.