Rather than convert the new lines, we can think of a single new line as a field separator and a pair of new lines as a record separator. With that view, we can accumulate the fields and then display them in the desired (comma delimited) format once we reach the end of the record.

#!/usr/bin/perl

use warnings;
use strict;

my(@accumulate) = ();

while (<DATA>){
    chomp;
    if (/^\s*$/) {
        print join(',', @accumulate), "\n";
        @accumulate = ();
    }
    else {push(@accumulate, $_)}
}
if (@accumulate) {print join(',', @accumulate), "\n"}


__DATA__
1111
2222
3333

4444
5555
6666
[download]