Obligatory standard response:

use strict;
use warnings;
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This will encourage you to write better code, in particular declaring all of your variables as lexical.

use CGI;
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It is much better to use the CGI module to handle your output, rather than rolling your own. For a discussion of this, see one of the great ancient works of the monastery.

use CGI::Carp qw/fatalsToBrowser/;
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This enables you to see your script's fatal errors in the browser. Essential for debugging.

Finally, checking the error given by system would probably be helpful:

my $err = system("who",">>/var/www/cgi-bin/new.txt");
unless ($err == 0)
{
   die "who command failed: $?";
}
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See the documentation for system for more information on checking the error codes.