There are plenty of technical reasons to use them (especially the security issue mentioned by Dan Beam).
What you shouldn't do is use iframes “like frames”, doing navigation to new pages by updating the iframe only. As you say, this prevents the navigation from being bookmarkable/linkable, responding to the normal navigation buttons, and providing useful link affordances like open-in-new-tab.
But that's not peculiar to iframes. You can see more and more pages where the navigation is done by fetching new content with XMLHttpRequest and writing it to the main content div's innerHTML. Often this is done with jQuery load() and clever-clever slidey animations. This breaks navigation just as badly as iframe-used-as-frame, or indeed old-school framesets. It's a shame so many web authors are using this tactic believing it to be a super-modern web design methodology, when really it's just a new skin on yesterday's despised framesets.
You can work around it in both cases, but it means you have to store a viewstate in the # fragment identifier part and support proper hash-navigation, which isn't trivial. Even then you've still got problems with non-JS agents like search engines; you end up having to have a parallel ?-based and #-based navigation to support both. It's a pain and most don't bother.
