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"So it's not a good idea to start adding some baptism keywords to product descriptions and such (but not remove any existing christening keywords)?"

No, you'll run the risk of cannibalizing your christening rankings and moreover may confuse your customers. Remember, develop for your customers NOT for the search engines.

For example, I work for a law firm and our homepage ranks for all sorts of criminal crimes (DUI, Drugs, etc.) So if I see an area where I want to improve my rank, say for "criminal defense attorney" - I'll write new content for a blog post or page around that set of KWs instead of trying to get the homepage to rank for that KW among all the others.

Yea, I have found and tested the fact that Google has essentially de-valued Comments, Footers, and Sidebars. To what extent I don't know. I wouldn't cease any natural blog commenting as it is just that, natural.

My comment was merely regarding the value (weighting) of different types of links. A blog comment link is worth much less than a link in the body or content section of the page. And because of this it could lead to your inside pages being considered more authoritative.

It's not that the homepage is being penalized or looked upon negatively, it just doesn't have the same inbound link juice.

Could it be something else, like a Panda update?

I agree, a typical negative SEO campaign in my mind is a ton of easy to acquire links. I doubt anyone is going to take the time to email webmasters and have links pulled.

I would look at your content stats in GA for YTD and see if you can see any trends for the pages that lost rank (or was it the homepage?).

Unless the negative campaign is targeting individual pages then I would assume the whole site would be affected.