Are we just talking the U.S. here??
Because I'm surprised nobody's brought up the differences between the U.S and Europe on this matter. Manuals are already dead among American manufacturers as far as I'm concerned (oh, sure there are a few models you can still get--GTO, Corvette, Viper). And I've also come across the number that 10% or less of cars sold in the U.S are manuels. But in Europe, where BMWs and Porshces are made, the trend is the exact opposite--10% or less of the cars have automatics. Sure, the option exists nowadays, but few Europeans buy their cars with autos. You'd be surprised by how many E-class (yes Mercedes does make manuals!) and even A6/A8 manuals there are in Europe. And given that fuel costs and efficiency are HUGE concerns in Europe and Asia, and I'm willing to be that buyers will be buying manuals on those continents for decades to come; also, it's kind of a cultural thing for them, too--just one more thing for them to differentiate themselves from "lazy" Americans.
Given this--just because manuals make up only a small portion of U.S. autos, but a major portion of Europe (also Asian cars)--I don't think the manual is dead or on the verge. Many have written that SMG/F1-style trannys will replace manuals. Sure, maybe in Ferraris (even that's a stretch) or BMWs, but I doubt Peugot or Citroen or Opel will be offering them any time soon.
Look at the bigger (brighter) picture guys....