Inside Dropbox, I have several folders relating to various things (Pictures, Music, Documents, etc.) The most interesting are:
Resources - A folder where I keep all my resources. This basically means my KeePass database, various fonts and web templates I've bought or collected over the years, my .emacs and vimrc files, and various other software resources.
Software - Here I keep all my portable software, the stuff I have to have on me to use a computer without pulling my hair out in frustration.
Projects - All my software projects (I have a separate "Graphical Projects" folder for graphical stuff, etc.).
Inside Projects, I have several folders by project name. These are arranged like so:
ProjectName/ <- Root, holds any subfolder with anything related to the project.
ProjectName/db <- Hold the sqlite database, which I usually use on my personal computer (most projects are Python/Django).
ProjectName/site_media <- Holds my static and dynamic media for Django projects. Static Media holds symlinks to the actual project folders.
ProjectName/repos <- Holds all the repos.
ProjectName/repos/main <- The main source code repo. Mercurial is used for SCM.
ProjectName/repos/design <- All my design-related documents.
ProjectName/repos/* <- Any other copies of my main for fixing small bugs and trying new things. I use Mercurial, so this is a standard practice.
And this is how the actual project folder looks:
ProjectName/repos/main/* <- All the files related to environment, for example, my Sublime Text project file, .bat files to automatically start the Django server, .hgtags and .hgignore, etc. Basically, things that are "meta" to the project, and not actual source code. Makes for good separation.
ProjectName/repos/main/.hg <- Mercurial folder
ProjectName/repos/main/project_name <- The actual source code
Hope that helps.