I've put much thought into how I organize my home directory. This is what I love most about using a lightweight, highly customizable, geeky and elitist operating system. You won't be able to reproduce this system with a mainstream OS without figuring out how to tell your applications to let go of the default (and sub-optimal) directories. The system is planned for fast to typing on the command line and is also quite french/english bilingual. The most important innovation is the elimination of a "documents" folder in favor of a resources and a production directories. Also, the pictures library is future proofed, relying strictly on the filesystem for it's structure.

######## Utilities

tmp/            Downloads, inbox, short lived files
bak/            Backup of configuration  files,  useful  to  have
                 during software updates to allow rollbacks. This
                 is not my actual full system backup.
bin/            Scripts, binaries.

######## Work

prod/           Production, things I created or worked on.
     art/       Things I made for myself, sorted by media, then
                  by date and title.
     */         Other directories are named after companies and
                  people's names for whon I did work.
res/            Resources, work from  other  people,  downloads
                  to keep, collections, manuals,  source  codes,
                  ebooks, databases.
wip/            Work in progress. This directory  allows  quick
                  access to projects I'm currently  working  on.
                  It can also act as a task list. Projects  can
                  move to and from prod/.

######## Multimedia

   m/           Music
   p/           Pictures (see next section)
   v/           Video (movies). I delete them or burn them on
                  a DVD to keep the directory small enough.

######## Multimedia/Pictures

Much inspiration from www.organizepictures.com
All entertainment/nostalgia pictures go in ~/mm/p.
This directory is split in categories  such as events,
collection, outbox, wallpaper. The  camera  is emptied
in the tmp/ directory then images  are  processed  and
organized. When a category gets larger, it is split in
years subdirectory. The personnal library is  the most
important so years directory for this one are directly
on the ~/mm/p/ level. Events directories start with an
ISO9660 date  and  the  format  is  uniform  for  easy
parsing and scripting.

0/              Undated/old pictues from childhood
    yyyy-mm[-dd].location.event_description/*.jpg previews
                               1/*.NEF       raw originals
                               4x6/*.tiff          exports
                               web/*.jpg        compressed
                               wallpaper/*.png conversions
outbox/         Hard links to images in above subdirectories
wallpapers/     Hard links to images in above subdirectories
collection/     Cool/interesting downloads to keep
tmp/            Temporary directory for camera dump

Other resources on the subject: