I have a folder called "GRAPHICS". Off it I have "terragen", "world machine", "lightwave", "photoshop", etc. Then I have sub-folders off those but not specific format.
Lightwave has a default content directory that works fine so I stick with it. For Terragen, I simply add a folder with a project name and feed everything used in that project into that one folder (Poseray can feed obj's and copies of texture images it gets (usually from Lightwave.) World Machine gets a "content" folder and in it will be "7may10a.tmd, 7may10b.tmd, etc" and the resultant output, like "7may10b.ter".
For programming I have a "PROGRAMMING" folder with all different languages I use, like "c#", "cpp", "python", etc. Again, I arrange the subfolders to these depending on how the compiler "likes" to output results.
So basically, a main category in all caps and actual apps. in lower case.
Oh, and backups. A simple second drive with the main categories (GRAPHICS, etc.) and zipped archives so I can replicate back to my main or replacement drive.
Whatever works for you and make an effort to stick to it (and clean it up every once in a while.)