With Summer '14 moving things from HTML Areas to VisualForce Areas one problem I've seen is that links in the iframe won't work properly. Since they are in the iframe they load in the iframe, not in the browser as a whole.
Is there a workaround for this? I might create a sidebar component as a VF Area component and it has a list of links to other records, for example. The intended behavior would be that I could click on a link and it would load as the main page. The current behavior is that it would load in the sidebar/iframe.
The problem also exists if you link to something from a Visual Force Console Component, which is the same basic problem of SFDC making everything live in an iframe.