...
use Tk;
use Win32::API;

# Windows constants
my ($OnTop, $NoTop, $Top) = (-1, -2, 0);
my ($SWP_NOMOVE, $SWP_NOSIZE) = (2, 1);

...

# Create a Win32::API object for SetWindowPos
my $SetWindowPos = new Win32::API("user32", "SetWindowPos", [N,N,N,N,N,N,N], N);

...

my $w = new MainWindow;

...

# do the 'always on top' bit
my $hwnd = $w->frame; # frame returns a hex value as a string, e.g. "0x1234"
print "$hwnd\n";
$SetWindowPos->Call(hex($hwnd), $OnTop, 0, 0, 0, 0, $SWP_NOMOVE | $SWP_NOSIZE);

MainLoop;