$ cat wire.pl

#!/usr/bin/perl

# Read all lines into @lines
my @lines=<STDIN>, @order, $n, $m, @l;

for($n=0; $n<=$#lines; $n++)
{
        if($lines[$n] =~ /[$]var[ \t]*wire/ &&
                (index($lines[$n], "[")>=0))
        {
                @order=();

                # Generate a list of lines like
                #       b       index   linenum
                for($m=$n;
                        $lines[$m] =~ /[$]var[ \t]*wire/ &&
                                (index($lines[$m], "[") >= 0) &&
                                ($m <= $#lines);
                        $m++)
                {
                        $lines[$m] =~ /([a-zA-Z]+)\[([0-9]+)\]/; # Extract name and index
                        $order[$m-$n]=sprintf("%s\t%06d\t%06d", $1, $2, $m); # Store in @order
                }

                # Sort the list in reverse order ( direct from perldoc -f sort )
                @sort=sort  {$b cmp $a} @order;

                # Skip these lines next loop, they'll be printed already
                $n=$m-1;

                # Iterate over our sorted list, extract line numbers,
                # print lines
                for($m=0; $sort[$m]; $m++)
                {
                        @l=split(/\t/, $sort[$m]);
                        print @lines[@l[2]+0];
                }
        }
        else    {       print $lines[$n];      }
}

exit 0;

$ ./wire.pl < data.wire

$date
Mon Aug 20 12:40:08 2012
$end
$version
version 9.5-hbe-sp-mm
$end
$timescale
1ps
$end

$scope module MAIN $end
$var  wire 1 i b[3] $end
$var  wire 1 h b[2] $end
$var  wire 1 g b[1] $end
$var  wire 1 f b[0] $end
$var  wire 1 e a[3] $end
$var  wire 1 d a[2] $end
$var  wire 1 c a[1] $end
$var  wire 1 b a[0] $end
$var wire 1 j cin $end
$var wire 1 k cout $end
$var wire 1 l gnd $end
$var wire 1 m gnd! $end
$var wire 1 n ground $end
$var wire 1 r sum[3] $end
$var wire 1 q sum[2] $end
$var wire 1 p sum[1] $end
$var wire 1 o sum[0] $end
$var wire 1 s vdd $end
$scope module x_adder $end
.......
....
#any such occurrences anywhere in the script

$