As a web application developer, I liberally use inline comments (code at the header and inline with code). It's a key to maintaining the code over long periods of time (we forget what we did and why) and across teams (somebody else may need to update code I originally wrote).
That said, I use comments surrounded with tags that do not end up in the HTML code rendered to a visitor. Most languages that "create" HTML code as output (ColdFusion, PHP, etc) usually have tags so comments can be used without being seen in the HTML.
In my opinion, this is the way to go.
Neil, you're probably concerned with the comments in HTML comment tags. I cannot help you there. For those of you who can suggest best practices to site owners and developers, ask that whenever possible inline comments are in tags that **do not show up in final HTML. **
Also, as a practice, I do not want the World seeing (or reverse-engineering) my code based on my comments. Use them as a web developer yet hide comments in output so SEOs do not have headaches of wondering how it affects rankings/page performance.
I hope that helps.