I've never really gotten into the whole 3D file navigation thing (ever since "It's a Unix system! I know this!", it's seemed pretty corny), but BumpTop might be the exception I've been waiting for. It's a 3D overlay for your OS X desktop that turns files into 3D objects to move around, pin on the walls, pile up or break down as needed. It's not too shabby -- with all of these things, there's a fine line between adding in graphic splashes for the heck of it, and making sure everything has a real function, and it seems like BumpTop walks that line pretty well. Most of the graphical flair does actually help with a function also. The app also supports the multitouch trackpad on MacBooks, so there's a little bit of innovation to play with as well.
Mashable says BumpTop is planning even more integration in the future, piping content from sites like Facebook and Twitter straight to one of the desktop's walls, and more involvement with the touch interface, even as we await the tablet's announcement.
I don't know if it's quite enough for me to leave behind the 2D icons and filenames that have worked well so far, but BumpTop is an interesting experiment in adding that third dimension into your normal workspace. The app is a free trial download, with a Pro version available (multitouch support, unlimited stickies, instant search) for $29.