If you look at the direction many manufacturers are going with transmissions for higher performance models, it would seem that clutchless manual transmissions will be the future.
Looking at racing, F1 and many sports cars in ALMS and Grand Am use clutchless transmissions with paddle shifters. Ferrari in particular, has made its clutchless transmissions lightning fast. The new Nissan GT-R has gone this route too.
Volkswagen and Audi have taken this technology and have allowed it trickle down to lesser models like the GTi. As more and more consumers want more and more sophistication and luxury in their cars, manual transmissions will decline.
Let's face it: Having the benefits of a manual transmission and an automatic combined into one has quite an appeal. Being able to switch between modes is an attraction for many, especially when caught in stop and go traffic.
I for one though still long for a manual transmission. There is something about the interface between using the clutch, applying gas and rowing through the gears that is immensely satisfying. I would be sad indeed if they were discontinued. I don't see this happening anytime soon however.