Here are some minor suggestions:

• Allow the data to be specified on the command line. Having to type the values on separate lines can be inconvenient in some situations.
• Turn on warnings.
• Handle EOF (or an error) when reading from STDIN.
• Environment variables are usually given a value type of REG_EXPAND_SZ (instead of the default REG_SZ that you used) so that they can be, for example, "%SystemRoot%\\system32".
• Check for failure on the insert.

#/usr/bin/perl -w
use strict;

my $Reg;
use Win32::TieRegistry ( 
    TiedRef => \$Reg, 
    ArrayValues => 1, 
    Delimiter => '/', 
    ':REG_' 
);

my( $Host, $Key, $Value )= @ARGV;

# Asking for machine name and info to be added to the sys env var
if(  ! defined $Host  ) {
    print "What host would you like to connect to? ";
    $Host= <STDIN>  or  exit;
    chomp $Host;
}
if(  ! defined $Key  ) {
    print "What name would you like for the Sys Environment Variable? 
+";
    $Key= <STDIN>  or  exit;
    chomp $Key;
}
if(  ! defined $Value  ) {
    print "What value would you like to assign to this variable? ";
    $Value= <STDIN>  or  exit;
    chomp $Value;
}

# this is the system environment variable area done on the registry
my $SysEnv= $Reg->Connect("$Host", "LMachine/System/CurrentControlSet/
+Control/Session Manager/Environment/") 
    or  die "Can't connect to $Host 's registry or can't open Registry
+ key, Session Manager/Environment: $^E
+\n";

# create a new value and set its data
$SysEnv->{"/$Key"} = [ $Value, REG_EXPAND_SZ ]
  or  die "Can't create $Key ($Value): $^E\n";
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