Don’t “organize” them. Use search. Clear your desktop, clear your mind.

1. Put anything you download or create on your desktop.
2. Make a script that moves desktop files not accessed for x hours or days into a named folder, “{yyyy-mm-dd} - {computer name} {username}”, where that date is the date of the start of this seven day week. If you need something a couple days after you worked with it, just open the most recently weekly folder.
3. Backup that folder set. It’s very efficient to do even an online backup sync since only the current week’s folder will usually have any changes. (The unique machine name and username is so you can backup from multiple machines and accounts into the same backup location, letting you access all files within the same backup space.)
4. Use search to find what you need. (My OS-independent preference in order is X1 on Windows, Spotlight on Mac, latest Windows Desktop Search on Windows, and Google Desktop Search on Windows.)
5. If search doesn’t find it, your mind will find it relatively easy to find the appropriate week’s folder, as you can generally remember the sort of information flow of time to remember about when you worked on something.

Refine the above system based on your own work habits. For example I sweep files off the desktop within a couple hours “if not accessed within” time. Some colleagues I’ve helped with this use a 2 day “if not accessed within” time. Others don’t create or grab many files, they prefer a monthly folder to a weekly folder. Do not try to make a daily folder, however, because you’ll get too frustrated attempting to find something manually.

Tip:

 !/usr/bin/perl
use POSIX qw(strftime);
$sundaystring = strftime “%F”, localtime(time + (( 7 - (localtime(time))[6] ) %7) * 60 * 60 * 24 );