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A lot of companies out there that offer search engine promotion will throw every type of HTML tag they can into their page in hopes of it giving a helping hand. Comments, drop down lists, forms, etc. So much of it that they lose track of what they did that actually boosted the page.
<!-- <h1>keywords here</h1> -->
I think it is most likely ignored, but I know several SEO firms that still use it. I would be interested in hearing if anyone feels that placing html tags within a comment makes any engine index it.
When you consider the fact that only a very small percentage of the pages in a particular index use comments for SEO purposes, I think it would be fairly obvious that you would probably end up doing more harm than good if you attempted to add a penalty.
Simply ignoring them eliminates the potential abuse without penalizing the sites that truly use comments for there intended purpose.