The problems are not in the declaration, but in sub ThrowMyException. Here is a working version, with changes commented:

#! perl
use strict;
use warnings;

use Exception::Class
(
    'MyException',

    Commands =>
    {
        isa         => 'MyException',
    },

    Timeout  =>
    {
        isa         => 'Commands',
        description => 'This exception results from running the metric
+s commands',
    },

    DBError  =>
    {
        isa         => 'MyException',
        description => 'DB returned error',
    },
);

ThrowMyException();

print "No error caught\n";

sub ThrowMyException                # NO prototype
{
    eval {
             Timeout->throw         # NOT MyException::Commands::Timeo
+ut->
             (
                 error => "This error is due to a timeout"
             );
         };

    my $err;

    if ($err = Exception::Class->caught('Timeout'))
    {
        die $err->description .     # NOT $err->{"description"}
            ': ' .
            $err->error;            # NOT $err->{"error"}
    }
    elsif ($err = Exception::Class->caught('MetricsException'))
    {
        die $err->error;
    }
    else
    {
        $err = Exception::Class->caught();
        ref $err ? $err->rethrow : die $err;
    }
}
[download]

Output:

12:30 >perl 517_SoPW.pl
This exception results from running the metrics commands: This error i
+s due to a timeout at 517_SoPW.pl line 56.

12:33 >
[download]

Hope that helps,