In his article of Feb 12, responding to the same article as I have just done, Ryan Muldoon seems to share the notion that we need to be a little more revolutionary in our approach to interface design.
He mentioned Nautilus, a program I've been testing rather extensively. I'm also very excited about the prospect of a GUI made of many useful components accessible from a single graphical shell. It helps "get the interface out of the way" since users don't have to remember what application they need to use to accomplish a given task. And of course, as they say, sometimes the best interface is no interface at all -- which is where autonomous agents enter the picture.
Ryan also mentioned file systems and metadata. For some reason, I have this persistent vision of a filesystem built on a relational database, which perhaps works in concert with a search engine and a traditional file hierarchy (which could be integrated with the database to provide unambiguous but human-readable descriptors). You might want to ask your computer to get "that slideshow from last week for work" or to show "that e-mail from Susan yesterday about the usability testing." Interestingly, Evolution is starting to integrate some of this functionality, for e-mail at least, with the "Virtual Folders" feature. Alas, there will not likely be an NL front-end any time soon.