perhaps you could work with something from the command line like

for i in `find . *.txt`; do perl -pi -e 's/\n/,/' $i; done;
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update or maybe a Perl only solution. This one uses recursion to traverse subdirs.

#!/usr/bin/perl

use strict;
use warnings;

my $dir = ".";

lista_dirs($dir, $dir);

sub lista_dirs {
    my ($dir, $dirname) = @_;
    my (@dirs, @files);

    opendir DIR, "$dir";
    my @dircontent = grep { /[^\.]/ } readdir(DIR);
    closedir DIR;

    @dirs  = ();
    @files = ();

    foreach(@dircontent) {
        if(-d "$dir/".$_) {
            push @dirs, $_;
        } else {
            push @files, $_ if($_ =~ /\.txt$/);
        }
    }

    foreach my $d(@dirs) {
        lista_dirs("$dir/".$d, $d);
    }

    # IMPORTANT NOTE: if your files aren't too big, you can read every
+thing at once as shown in the code below.    # if note, you can open 
+the input file for reading and a temp file for wirting. Read the file
+ line by line,     # replace \n with the , and write to the temp file
+. Close both files when you're done, and then 'rename' 
    # the temp file to the input filename
    foreach my $file (@files) {
        $/ = '';
        open FILE, "$dir/$file";
        my $content = <FILE>;
        close FILE;

        $content =~ tr/\n/,/;
        open FILE, ">$dir/$file";
        print FILE $content;
        close FILE;
    }
    return;
}
<p><b>update 2</b> After reading the other replies I realized I misrea
+d the question, and there was no need for recursion, so the solution 
+came to be more complex than it needed to be. I was really in the nee
+d to get some sleep.</p>
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