How should I organize my source tree?

I am an individual developer working, largely, on web-projects (W/LAMP) and, at times, on C/C++ (non-GUI) projects of about average scale.

I often struggle with structuring my source-code tree. In fact, usually, I don’t complete a project without dumping the entire tree and rearranging the pieces three-four times which really takes up a lot of effort and moreover the end result does seem like a compromise.

Sometimes, I end up with over classification of source – very long tree of folders and sub-folders. At other times, I simply end up concentrating all files in a particular folder based on the larger purpose they serve and thereby leading to ‘chaotic’ folders in the source.

I would want to ask:

• Are there any principles/logic/best-practices that can help me better at structuring my source tree?
• Are there any graphical/diagrammatic techniques (for eg.: DFD in case of dataflow) that can help me visualize my source tree beforehand based on the analysis of the project?
• What strategy to adopt to structure multi-media files-tree associated with the project?

About the bounty: I appreciate existing answers with the members sharing their own practices, however, I’d like to encourage more general and instructive answers (or resources) and more responses from the members.