Tools/Techniques to use our ability to think spatially

What software/UI techniques can leverage our spatial memory? I think and remember in physical space, often the location of something is as important as it's content. For instance I keep an untidy desk, but I know where to find things, I use different parts of my (multiscreen) desktop for different windows/icons. I annotate books (with post its) and can remember facing page, top/bottom etc. In the good old days we used to file things so we could find them later, now we use search, but that doesn't really use our spatial abilities. Google maps etc are brilliant but they're only really being used for the real real world, what about our internal locations? How can we leverage the wet ware to best advantage.

EDIT -> I've thought about a cod开发者_开发百科e tool that would profile the running code and then build a visualisation with classes/methods scaled to match their use, with large/small motorways/footpaths between them. Spatial layout still escapes me though - UI at the top, DB at the bottom, but how do you position a class in 3D based on it's usage?

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Slightly off topic since it's not code per say but I've built my own tools to translate some of out complicated XML config files into DOT format and run them through Graphviz so that I could visualise them. We were able to strip out lots of pointless stuff from them after just looking at them.

Wetware win :o)