One way to arrange things in 2 rows of 3 each is to divide your area into 2 Tk::Frames:

Red  Green  Blue	<-- Top frame
Mustard  Vinegar  Salt	<-- Bottom frame

Then pack each row into its frame, left-to-right:

my $mw = new Tk::MainWindow;
my $top = $mw->Frame->pack;
my $bottom = $mw->Frame->pack;
my @cb = ((map { $top->Checkbutton(-text => $_)->pack(-side => 'left')
+ }
       qw{Red Green Blue}),
      (map { $bottom->Checkbutton(-text => $_)->pack(-side => 'left') 
+}
       qw{Mustard Vinegar Salt}));
MainLoop;
[download]

Of course, this keeps the widths of different buttons independent. If you want everything nicely gridded out, use the Tk::grid geometry manager instead of Tk::pack. This lets you align everything, a bit like this:

Red	Green	Blue
Mustard	Vinegar	Salt

You'll probably want to stick each Checkbutton to the east side of its box, too:

my $mw = new Tk::MainWindow;
my @cb = ((map { $mw->Checkbutton(-text => (qw{Red Green Blue})[$_])->
           grid(-column => $_, -row => 0, -sticky => 'w') } 0..2),
      (map { $mw->Checkbutton(-text => (qw{Mustard Vinegar Salt})[$_])
+->
           grid(-column => $_, -row => 1, -sticky => 'w') } 0..2));
MainLoop;
[download]

---

ariels -- Add table to explicate the thing with the grid.