As far as new inovations... hm... well the piezo pickups have been around for quite some time... the earliest I can recall is since Slash used one in his Gibson Les Paul in the early 90's. The Steinberger guitars are pretty ahead of their time I think... I like the moving capo that they put on the end. That's pretty slick. The fact that they had the presence of mind to make it on a baritone scale guitar is that much better. You just roll the capo up two frets and it's in standard tuning... roll it back to the end and you're dropped down a whole step...
I think the biggest strides the last few years have been on engineering better sounding guitars. Some different concept guitars have been released... One company has been making guitars out of a new material called Vibracell... and Yamaha has made a new guitar out of some wierd material and have used an enigineered chambered body to help it resonate more than any other electric out there.
Floyd Rose came out with there speedloader guitars that load and tune from the other end....
And Steinberger makes gearless tuners now.... check those out at stew-mac.com. They're pretty smooth looking.
As far as acoustic guitars go... I would have to say that they're going to stay mostly unchanged for quite awhile. But Taylor has tried to make a stride toward some new innovations with their T5 series of guitars... They mix electric playablity with acoustic tone...
Not a lot has changed in regular pickup configuration in about a decade... but manufacterers keep producing more specialty pickups that are basic variations of the same old pickups we've always known.
I did see a guitar with an onboard preamp and onboard effects.... But I guess the biggest thing in guitars to me right now is the new Line 6 Variax modeling guitars. Coupled with the software you can model any guitar you want pretty much and it allows you to change pickup configurations and all that jazz...