On my checklist is written that "all documents must be accompanied by an explanation as to what each document is and how is relevant to your visa application. Related documents should be grouped together and where appropriate, dates of periods of time should be clearly marked on the documents."
I'll probably attach A4 explanation with a paper clip on every document and where appropriate use highlight marker for the dates on the document.
I'll have one folder for forms and documents (copies of passport, birth certificates), and the other for stat. decs and statements accompanied with all relevant documents, and then third one with letters, postcards, christmas cards...