I used to accumulate folders all over my desktop and over time, it became difficult to find what I needed. I've found a way to make a little easier to find my stuff quickly. It revolves around three elements:
1. A core visual on my desktop that helps to organize folders according to key work-related tasks. I use Cmap to do the diagram.
2. Shortcuts to folders I need to access most often
3. Regular review and reorganizing based on how work is evolving.
The diagram below is based on my real world job.