I sometimes short circuit while or for loops with something like:

while (<FILE>) {
  chomp;
  s/^\s*#.*//;  # remove comment-only lines
  next if /^$/; # skip blank lines (or, commented out lines)
  do_something_with($_);
}
[download]

This turns comment-only lines into blank lines, and then skips any blank lines in the file (not just the last line of the file).

Is this what you're looking for?

Alan