I must seriously be missing something about references or objects or TiedHashes excetera

No, that part was fine. There are plenty of problems, however.

• I have no idea what = $error is doing in
  Dumper %RegHash = $error;
  and you discard Dumper's output. Did you mean
  print(Dumper(%RegHash));

• @set = 2
  should be
  @set == 2

• $error is printed, but nothing is ever assigned to it.

• each returns false when there is no more data (which is not an error), so
  each %RegHash or die
  can't be right. Anyway, it's easier to work with foreach keys than while each because since can only use last safely with the former.

• Why do you store a key in a variable called $val? $key would be better. $class would be ideal.

• $watchcode isn't reset for each class, but it should be.

• You print $! when it doesn't contain anything meaningful.

• To use die when you can't find an association is quite brutal. warn (and maybe nothing at all) would be more appropriate.

Fix:

#!/usr/bin/perl

use warnings;
use strict;

use Win32::TieRegistry (Delimiter => "/");
use Data::Dumper;

foreach my $class (keys %{ $Registry->{"Classes/"} }) {
    next unless substr($class, 0, 1) eq '.';

    my $watchcode;

    my $RegHash = $Registry->{"Classes/$class"};
    foreach my $key (keys %$RegHash) {
        next if $key ne "/";

        my $val = $RegHash->{$key};
        print "$class = $val\n";
        $watchcode = 1;
        last;
    }

    warn "failure to recognise association list\n"
        unless $watchcode;
}
[download]

Notes:

• I used next (twice) to avoid excessive nesting/indenting.

• I added last in the inner loop. It's no use searching for a second key called /.

• I made $RegHash a reference instead of an actual hash (%RegHash). It's much more efficient to refer to something than to make a copy of it.

Update: Fixed reference to $key that wasn't changed to $class (my mistake). $key swapped with $val (OP's mistake).

Update: The inner loop can be replaced with ifexists.

foreach my $ext (keys %{ $Registry->{"Classes/"} }) {
    next unless substr($ext, 0, 1) eq '.';

    my $RegHash = $Registry->{"Classes/$ext"};

    if (not exists $RegHash->{'/'}) {
       warn "Unable to recognise association list for $ext\n";
       next;
    }

    my $class = $RegHash->{'/'};
    print "$ext is a $class\n";
}
[download]

Tested.

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