The most important objective when organizing files is to consider find-ability and making day-to-day work easier to manage.
In order to make computer files easier to find later, it's good to start with a project management approach. For me that consists of keeping a spreadsheet or database of projects with corresponding project numbers. If I faithfully record my projects, later, I can do a simple search by job number, project title, or kind. And if I place that project number on the finished project itself it's even easier to rediscover the original project files later.
No matter what method you use to track your projects this is where you need to start.
To organize your computer files in a manner that makes working easier and faster, consider creating category folders. For instance, if you do web and electronic work, illustration, and print it's a good idea to keep separate folders for each kind of work. And within these folders create a subfolder you can use as a template. Whenever you start a new project just copy this template folder and give it the name and project number of the new job. (I always put the number before the project title, so that the projects remain in numerical order.)
For print and illustration you can create a template folder with the subfolders Documentation, Final Files, and Working Files & Versions. The Documentation folder can contain any information pertaining to the project such as copies of email correspondence, files from clients, and notes and specs. The Working Files folder contains the files you use for creating and working on the project, and for storing any previous versions. The Final File folder contains the final project files.
This method is super useful because you not only will be assured you will be able to understand what you did years later, but someone else will be able to work on a project you had previously created.
There is much more I can say, but thought I'd share these little techniques I find useful.
Photo courtesy Renjith Krishnan of freedigitalphotos.net