Playing with groups.google.com I understand that <<Unix window managers do not have such a "Always on top" feature. To be more precise, most Unix window managers can do something like "Always on top", but there's no X11 standard.>> (from Slaven Rezic) From Slaven, the (untested) trick is:

$top->bind("<Visibility>" => sub { $top->raise });
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For win32, with a trick by Toby Everett, for me works this:

use strict;
use Tk;
use Win32::API;

my $mw = new MainWindow;
use vars qw/$Button/;

$mw->Frame(-width=>200, height =>25);
$mw->update;
  Win32::API->new("user32","SetWindowPos",[qw(N N N N N N
N)],'N')->Call(hex($mw->frame()),-1,0,0,0,0,3);


$Button=$mw->Button(-text => "Button",
        -command => sub {
                &do_something;
            })
        ->pack();


MainLoop;

sub do_something {

    #sleep(10);
}
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UPDATE:
Always from Slaven Rezic, there is a trick for KDE2:

If you're using KDE2 the you can write following ($w is your toplevel widget):

    my($wrapper) = $w->toplevel->wrapper;
    $w->property('set', '_NET_WM_STATE', "ATOM", 32,
         ["_NET_WM_STATE_STAYS_ON_TOP"], $wrapper);
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I think the _NET_WM_* stuff is also GNOME-compliant.