It depends. For throwaway scripts, I might put HTML inline using HEREDOCs, or I might embed a trivial HTML template after __END__. For anything other than throwaway, I tend to use HTML::Template, which allows the HTML to be edited separate from the code.

Two big problems with mixing HTML and code are:

1. Non-coding HTML designers are shut out. They can't edit the HTML without risk of breaking code.
2. Developers are usually marginal designers, at best.