opendir(DIR, "c:/$directory") ...
                ^
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For extra credit, explain what, if anything, this has to do with CGI.pm

In that case, chomp will remove the \n, but there will still be a trailing \r at the end of the filename.

Your error message ought to print "Cannot open $directory" and then the contents of $!. Since you're only getting $!, if you've reported the entire error message, it indicates that Perl printed the first part of the error, hit the \r, moved back to the first column, and printed the second half:

my ($one, $two) = qw( one two );
print "$one\r$two\n";
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As a side note, I usually debug variables by printing them like print "Directory: ($directory)\n";. That helps make whitespace apparent.

You may want to try this instead of chomp:

$var=~tr/\n\r//d; $var=~s/^\s+//;
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--
$Stalag99{"URL"}="http://stalag99.keenspace.com";

use CGI qw(:standard);
#use Win32::ODBC;
use strict;
use win32;

my ($directory);
my ($name);

print "enter in directory \n";
chomp ($directory = <STDIN>);
print "directory is $directory\n";

#Open the directory to list what's inside 
opendir(DIR, "c:/$directory") || die "Cannot open $directory $!";
foreach $name (sort readdir(DIR)) { #Prints names sorted 
     print "$name\n"; 
} 

closedir(DIR);

print "$directory is the directory";
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