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Two-pane file managers (ex: GNOME Commander, worker) are so useful that it is strange they are not a default feature of file managers on all systems. Expending on a related subject, Overlapping windows look cool at the expense of years of productivity are lost in moving and resizing. Hopefully with the current of popularity of the iPhone and iPad, Tiling window managers (ex: i3, ratpoison, xmonad) might make a come back.

Innovative Interface awards go to Eagle Mode and CodeBubbles. There is no guarantee those interfaces will turn to be useful in mainstream usage but they are definitely in the "out-of-the-box thinking" category. If you are looking for more on the next age of programming, Bret Victor has written a very insightful article on Learnable Programming.

Otherwise Flowpaint and Scribus could find a place alongside the more famous LibreOffice, Gimp and blender in your application toolbox.