Seems to be PHAR related issue (once again) so the quick fix: disable phar. This is quite critical bug..

Please try this simple patch found at http://pear.php.net/~greg/fixbug46194.patch.txt

Index: ext/phar/phar.c
===================================================================
RCS file: /repository/php-src/ext/phar/phar.c,v
retrieving revision 1.370.2.45
diff -u -r1.370.2.45 phar.c
--- ext/phar/phar.c     13 Sep 2008 22:30:55 -0000      1.370.2.45
+++ ext/phar/phar.c     29 Sep 2008 13:00:22 -0000
@@ -3286,6 +3286,9 @@
        int failed;
        phar_archive_data *phar;

+       if (!file_handle || !file_handle->filename) {
+               return phar_orig_compile_file(file_handle, type TSRMLS_CC);
+       }
        if (strstr(file_handle->filename, ".phar") && !strstr(file_handle->filename, "://")) {
                if (SUCCESS == phar_open_from_filename(file_handle->filename, strlen(file_handle->filename), NULL, 0, 0, &phar, NULL TSRMLS_CC)) {
                        if (phar->is_zip || phar->is_tar) {

ok, it seems fixed with your patch, but i don't think it right. why filename can be NULL before it is past to compile file?
with php5.2-CVS cgi-fcgi:
No input file specified.
with php5.3-CVS and phar patch (or disable phar)
Fatal error: Unknown: Failed opening required '' (include_path='.:') in Unknown on line 0

something changed in cgi, many zend extensions might be affected

$ diff ~/src/php/php5.2/sapi/cgi/cgi_main.c  ~/src/php/php5/sapi/cgi/cgi_main.c
yeah... there are big changes
$ diff -u ~/src/php/php5.2/sapi/cgi/cgi_main.c  ~/src/php/php5/sapi/cgi/cgi_main.c |grep 'No input file specified' -C 5
+                       SG(sapi_headers).http_response_code = 403;
+                       PUTS("Access denied.\n");
                    } else {
-                       len += strlen(argv[i]);
+                       SG(sapi_headers).http_response_code = 404;
+                       PUTS("No input file specified.\n");
+                   }
+                   /* we want to serve more requests if this is fastcgi
+                      so cleanup and continue, request shutdown is
+                      handled later */
+                   if (fastcgi) {
--
-           if (errno == EACCES) {
-               SG(sapi_headers).http_response_code = 403;
-               PUTS("Access denied.\n");
-           } else {
-               SG(sapi_headers).http_response_code = 404;
-               PUTS("No input file specified.\n");
-           }
-#if PHP_FASTCGI
-           /* we want to serve more requests if this is fastcgi
-              so cleanup and continue, request shutdown is
-              handled later */


i'm not sure when will 5.3 cgi-fcgi prints out "No input file specified" which used to be print by 5.2, are you?

summary:
1. "Fatal error" just does not make sense here. it should be legal to pass any request including which might cause "404 File not found", from the webserver to php cgi-fcgi backend, and php should issue 404 error like 5.2 does

otherwise i have to set up
a. webserver(frontend) on server1 -> webserver + mod_php(backend) on server2, or
b. webserver(frontend, check-local=disabled) on server 1 -> webserver(backend, check-local=enabled to produce 404) -> php cgi-fcgi (backend)

2. passing file_handle == NULL || file_handle->filename == NULL does not make sense, it breaks zend extensions that hook zend_compile_file, like phar, apc, ZendOptimizer, XCache, Xdebug, eaccelerator, blahblah...

as you assigned it to phar category, i ask your advise

This bug has been fixed in CVS.

Snapshots of the sources are packaged every three hours; this change
will be in the next snapshot. You can grab the snapshot at
http://snaps.php.net/.
 
Thank you for the report, and for helping us make PHP better.

I'm marking this bug closed, as phar now handles stupid input correctly.  Please open another bug in CGI/CLI related category for the other problem.