#!/usr/bin/perl
use strict;
use warnings;

my $mycnt;
while(<DATA>){
    s!Number this.!++$mycnt.') Number this.'!ie;
    print;
}

__DATA__
Sample text.
Number this.
Number this.
Sample text.
Number this.

##</code><code>##

Sample text.
1) Number this.
2) Number this.
Sample text.
3) Number this.

##</code><code>##

Sample text.
a) Number this.
b) Number this.
Sample text.
c) Number this.
...