The solution I finally went with was similar to the following, near the top of all my scripts:

Perl:

open(STDERR,">>","/path/to/my/cgi-error.log")
    or die "Could not redirect STDERR: $OS_ERROR";

Python:

sys.stderr = open("/path/to/my/cgi-error.log", "a")

Apparently in Perl you don t need to close the STDERR handle before reopening it.

Normally I would close it anyway as a best practice, but as I said in the question, I have 269 scripts and I m trying to minimize the changes. (Plus it seems more Perlish to just re-open the open filehandle, as awful as that sounds.)

In case anyone else has something similar in the future, here s what I m going to do for updating all my scripts at once:

Perl:

find . -type f -name "*.pl" -exec perl -pi.bak -e  s%/usr/bin/perl%/usr/bin/perl
open(STDERR,">>","/path/to/my/cgi-error.log")
    or die "Could not redirect STDERR: $OS_ERROR";%  {} ;

Python:

find . -type f -name "*.py" -exec perl -pi.bak -e  s%^(import os, sys.*)%$1
sys.stderr = open("/path/to/my/cgi-error.log", "a")%  {} ;

The reason I m posting these commands is that it took me quite a lot of syntactical massaging to get those commands to work (e.g., changing Couldn t to Could not, changing #!/usr/bin/perl to just /usr/bin/perl so the shell wouldn t interpret ! as a history character, using $OS_ERROR instead of $!, etc.)

Thanks to everyone who commented. Since no one answered for both Perl and Python I couldn t really "accept" any of the given answers, but I did give votes to the ones which led me in the right direction. Thanks again!

For Perl, just close and re-open STDERR to point to a file of your choice.

close STDERR;
open STDERR,  >> ,  /path/to/your/log.txt  
  or die "Couldn t redirect STDERR: $!";

warn "this will go to log.txt";

Alternatively, you could look into a filehandle multiplexer like File::Tee.

Python: cgitb. At the top of your script, before other imports:

import cgitb
cgitb.enable(False,  /home/me/www/myapp/logs/errors )

(‘errors’ being a directory the web server user has write-access to.)

In Perl try CGI::Carp

BEGIN { 
use CGI::Carp qw(carpout); 
use diagnostics;
open(LOG, ">errors.txt"); 
carpout(LOG);
close(LOG);
}

use CGI::Carp qw(fatalsToBrowser);

python:

import sys

sys.stderr = open( file_path_with_write_permission/filename ,  a )

Python has the sys.stderr module that you might want to look into.

>>>help(sys.__stderr__.read)
Help on built-in function read:

read(...)
    read([size]) -> read at most size bytes, returned as a string.

    If the size argument is negative or omitted, read until EOF is reached.
    Notice that when in non-blocking mode, less data than what was requested
    may be returned, even if no size parameter was given.

You can store the output of this in a string and write that string to a file.

Hope this helps

In my Perl CGI programs, I usually have

BEGIN {
  open(STDERR, >> , stderr.log );
}

right after shebang line and "use strict;use warnings;". If you want, you may append $0 to file name. But this will not solve multiple programs problem, as several copies of one programs may be run simultaneously. I usually just have several output files, for every program group.