Web Development – The Line Between Code and Content?

markmcb asks: "I help design a LAMP web site and I’m constantly plagued by trying to decide on what level should I separate functional code and markup. Depending on what you read, some say embedding HTML in your PHP scripts [or Perl, or Java, or Ruby, or Python, etc] is bad while others say it’s no big deal. However, seldom are any practical applications of such code cited. How is your site