Nice! But...

use Digest::MD5::File qw(file_md5);
[download]

Ok, but then you're using Digest::MD5 instead, which indeed is loaded by Digest::MD5::File. You may just either use the former since it's a core module now or take advantage of the latter:

my $myfile = shift;
my $md5 =  new Digest::MD5;

$md5->addpath($myfile);
my $digest = $md5->hexdigest;
Win32::Clipboard::Set ($digest);
[download]

I would just either

Win32::Clipboard::Set
  Digest::MD5->new->addpath(shift)->hexdigest;
[download]

or

Win32::Clipboard::Set file_md5 shift;
[download]

in the two respective cases hinted above.

Oh, and I wouldn't print $digest; since we're putting that info in the clipboard anyway, but I would use wperl.exe instead. Of course an alternative would be a minimal GUI (e.g. Tk) showing the computed checksum, possibly along with a button to copy to the clipboard or compare with a value previously stored into it. However this would loose the fascinating simplicity/minimality of your solution...