We put stuff into computers (and, for that matter, get stuff out) in pretty much the same way we have for a good couple of decades.
Of course, we still use keyboards of a fairly standard design as our primary mechanism to feed words into a computer and mice are well-ensconced as the navigational tool of choice. Over in the gaming world, it's the familiar two-handed game controller that predominates. In fact, I sense that one sees fewer joysticks, steering wheels, various oddball keyboards, and trackballs than one saw in the past. This probably reflects that "productivity" PCs are shifting toward notebooks on the one hand and that gaming is moving toward consoles on the other.
The one clear counter-example is the emergence of "thumbing" (as opposed to typing). But this is really more about making compromises in service of the form factor of handheld devices than it is a genuine innovation--however commonplace it has become.
However, we may be starting to see some genuine change.
The motion-sensing Nintendo Wii remote isn't a particularly new concept. We've see academic work in data gloves of various types going back to the 1990s. What's different is that the Wii is mass market. Volumes mean not only lower cost, but an incentive for software makers to write games and other applications that support and use the device in interesting ways. Because it corresponds to the physical world, hand movement seems a natural fit with many tasks and manipulations. As a result, I expect that we'll see descendants of the Wii in increasingly widespread use.
Another big trend we're seeing is multitouch. As CNET News.com's Tom Krazit notes, it's Apple that has pushed this technology into the mainstream--starting with the iPhone in the handheld arena and the MacBook Air in the notebook space. (On the notebook, it's the touchpad rather than the whole screen that is multitouch and it's less of a big deal as a result.) I've been arguing for a while that being able to draw a "napkin drawing" or a "whiteboard sketch" is one of the things that's largely missing today when we work and collaborate remotely. The combination of multitouch and writeable LCDs at affordable price points, and supported by software, would be a genuine step forward.
These aren't the only possibilities. Six-degrees-of-freedom controllers have long been used in 3D engineering programs but they've been priced for the CAD professional. Logitech has come out with the affordable (about $55) 3Dconnexion SpaceNavigator PE (Personal Edition) 3D Navigation Device version that makes a great Google Earth companion. If 3D virtual worlds ever take off in a big way, devices such as these would be a natural and obvious fit.
Then there's always voice recognition. It's getting better. But that could be a statement for just about any year. And general-purpose voice recognition remains a niche. You won't catch me betting on it (although I suspect its time will come--someday).