The kind of "good" use you point to, "separating navigation from content", is actually problematic for SEO and almost certainly for usability and others too.
The problems, essentially, are those of value (PageRank, what have you) not being passed to the target of the iFrame, people arriving from search onto a piece of content without it's frame (and thus without navigation), and people not being able to link directly to content.
I should add, there's actually been some debate about about whether value is passed or not. However, I don't think anything conclusive came out of it and, even if value is passed, the other problems still make it unworkable.
Anyway, the SEO angle is covered quite well on another thread: Do we still need to avoid using frames and iframes for SEO?. I think the bottom line is there's no good reason for iFrames to form the basis of a site's design, and doing so introduces potentially serious problems for users and site performance. However, as Su' points out, there are still occasions where it's the right tool for the job.