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

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In reply to Re: how to convert new line to "," by eye
in thread how to convert new line to "," by bh_perl

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