One thing that changed my life is z, a utility to navigate easily to arbitrary directories based on frecency. Makes dir structure a bit less relevant; with z the distance between any two dirs is effectively constant.

https://github.com/rupa/z

     	By project, by tool? What do you do with pdfs and reference stuff, surely not Dewey Decimal?

~/proj ---> all my current projects and stuff i've pulled down from GitHub so I can examine it. usually 20 or so. subdirs for employer, etc

~/Dropbox/personal ---> scanned documents, receipts, etc

~/Dropbox/work ---> subdirs per client/employer

~/Dropbox/ebooks ---> organized into subdirs by topic

~/Dropbox/pdfs ---> web pages i've "printed" to pdf for archiving/reference. organized into subdirs by topic

~/Desktop/old ---> the "junk drawer" i occasionally clean out. doesn't get too big

~/Music ---> mostly just iTunes doing its thing

I also have a truckload of media (games, movies, music) stored on external hard drives since there's not much room for it on the internal SSD.