Having worked with them in many circumstances, I've really come to think that iframe's are the web programming equivalent of the goto statement. That is, something to be generally avoided. Within a site they can be somewhat useful. However, cross-site, they are almost always a bad idea for anything but the simplest of content.
Consider the possibilities ... if used for parameterized content, they've created an interface. And in a professional site, that interface requires an SLA and version management - which are almost always ignored in rush to get online.
If used for active content - frames that host script - then there are the (different) cross domain script restrictions. Some can be hacked, but rarely consistently. And if your framed content has a need to be interactive, it will struggle to do so beyond the frame.
If used with licensed content, then the participating sites are burdened by the need to move entitlement information out of band between the hosts.
So, although, occaisionally useful within a site, they are rather unsuited to mashups. You're far better looking at real portals and portlets. Worse, they are a darling of every web amateur - many a tech manager has siezed on them as a solution to many problems. In fact, they create more.