Make sure to start your script with strictures:

use strict;
use warnings;
use File::Find::Rule;
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For file names with spaces, wrap them with quotes. For example:

my $itunes = '"/Volumes/Media/iTunes/iTunes Media/Automatically Add to
+ iTunes/"';
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As for your $list, I would eliminate that and call File::Find::Rule in list context like:

my(@files) = File::Find::Rule
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Here's how I would do it:

#!/usr/bin/perl

use strict;
use warnings;
use File::Find::Rule;

my $handbrake = '/usr/local/bin/HandBrakeCLI';
my $preset = 'AppleTV';
my $itunes = '"/Volumes/Media/iTunes/iTunes Media/Automatically Add to
+ iTunes/"';
my $tvtag = '/usr/local/bin/tvtag-sickbeard.pl';

my(@files) = File::Find::Rule
    ->file()
    ->name( qr/\.(mkv|avi)$/ )
    ->in( @ARGV );

@files = join("\n", @files, '');
print "\nFound the following files to convert:\n\n@files\n";

foreach my $file(@files) {
    print $file . "\n";
    system "$handbrake -i '{$file}' -o '$file.m4v' --preset=$preset";
}
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