Based on the variable name, I thought you were only printing the host without the domain.

And when you said "skip it", I thought you meant the line, not the domain.

while (<DATA>) {
   my ($host, $domain, $test) = /^([^,.]+)(,[^.]+|)\.(.+)$/;
   $domain =~ s/,/./g;
   $domain = '' if /\.net$/;
   print("Host:$host$domain Test:$test\n");
}
[download]

Turns out

$domain =~ s/^.*\.net$//;
takes the same amout of time as
$domain = '' if substr($domain, -4) eq '.net';
but both are slightly slower than
$domain = '' if /\.net$/;

Update: 17% faster:

while (<DATA>) {
   chomp;
   my ($host, $test) = split(/\./, $_, 2);
   $host =~ s/,/./g;
   $host =~ s/\..*\.net$//;
   print("Host:$host Test:$test\n");
}
[download]

Update: If I change
$host =~ s/\..*\.net$//;
to
$host =~ s/\.my-domain\.net$//;
my version is 6% faster than yours (with $host =~ s/,/./g; added).

Update: Benchmark code

Great, thanks for that :)

I guess the lesson I've learned here is to never forget the kiss principle ;)

Cheers,
Darren :)

Okay... this one kept me awake last night :(

Because I'd still like to know... how could I have re-written the original expression to get rid of the unwanted commas?

Can somebody please put me out of my misery?
(I promise I won't use it in production :D)

Substitutions work by editing the string being matched, but you want the substitutions to work on the string being returned. That doesn't work.

You could do it with a parser, but Perl 5 regexp are not good enough to form a parser. (Well, it's theoretically possible with experimental regexp features.)