#!/usr/bin/perl -w 
use strict;

{
    local $/; 
    my $line = <DATA>;
    $line =~ s/\b\n\b/, /g;
    $line =~ s/\n{2,}/\n/g;
    print $line;
}

__DATA__
1,111
22,22
33,33

4,444
5,555
66,66



45,54
4,554
4,654
-----------

Output:
1,111, 22,22, 33,33
4,444, 5,555, 66,66
45,54, 4,554, 4,654