|I'm pretty sure that what I'm seeing for my own site is a phrase by phrase issue. Having said that, in my serps there are some whole sites that have suffered for all or at least many search terms. |
I'm just hypothesising that there is something related to anchor text on and off site and keyword stuffing in certain areas (types of tags like image alts for example) of pages that cause the term by term effect. Anchor text in sitewide links like the big footer on every page with links to "key" pages on the site may also be involved in this.
Then there's a different ssue that affects a whole site that is caused by link buying, hidden back links, links from certain networks etc.
If you have both then Ker-Bam! you're gone.