Back in the early 2000's using (i)frames was a big no no for developers. Although they made development easier, it was shunned in every circle and various reasons.
My question is, is it still advised not to use (i)frames? Although there are plenty good reasons to use them? ( e.g. separating navigation from content etc.)
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.
Personally, I have found that they still make some things easier. Although IE (Unfortunately still with one of the largest user bases) still has a lot of problems with javascript and it's many libraries and iframes.
Although with Ajax and re-loadable DIV's I find that it's a little redundant and that iframes are now pretty much obsolete. To my own personal usage at least.
