If you're planning to read through a list of files from the command line, then you should really use <> - it saves you all the work of opening all the files etc..

And, rather than all that work with $in_pod, I'd just use the range operator.

A line containing no alphanumerics is not counted as a line of code

Not sure I'd agree with that. Haven't you seen some of the JAPHs posted :) I'd personally check for absence of non-whitespace.

So, personally, I'd reduce all this down to:

#!/usr/bin/perl -w

use strict;
my $total = my $pod = my $comment = my $blank = my $code = 0;

while(<>) {
  $total++;
  if ( /^=\w+/ .. /^=cut/ ) { $pod++; next }
  if ( /^\s*#/ )            { $comment++; next }
  unless ( /\S/ )           { $blank++; next }
  $code++;
}

print <<END;
 Total:    $total
 POD:      $pod
 Comments: $comment
 Blank:    $blank
 Code:     $code
END
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Tony