Let the computer do its work. You can sort by date and search. There is no reason to bury your folders into sub-level after sub-level folder directories (try to stick to the no more than 3 level rule). Here is my system that I adapted from a lifehacker post Geek to Live: Organizing "My Documents" and GTD principels
@backup: for blog, contacts, email, etc. back ups
@docs: all your working files
@docs-archived: all files you are done with
@junkdraw: temporary holding place, good place to download temp files into
@multimedia: video, pics and music files, makes it easy to add to libraries
@scripts: code and shortcuts files
* Note I use the @ symbol to get these files names up to the top of a list when alphabetized.