I decided to use 2-pocket folders, like this. I filed all of the work in the left pocket and as we complete things they get placed in the right pocket. It is very easy to see what we still need to accomplish with this system. The index card paper-clipped to the left pocket is the Library List for the following week.
Behind that is a Shopping List for the following week. The index cards fit in my wallet perfectly, and it is so nice to just grab them when I go shopping and be assured that I have all of the items on hand for our science, art, and history projects!
The yellow post-it stuck to the SOTW Activity Book page pictured here lists the pages in the Usborne Internet-Linked Encyclopedia that correlate to the weeks' lesson. I stick it in the UILE as a bookmark at the beginning of the week and my son can read about the subject we're studying whenever he desires.
We have green for one child, blue for the other, and red for my files. The week number is in the upper left corner.
I also have yellow folders for each of the months of the year that I've put seasonal ideas, crafts, and notes in.
I have 36 hanging file folders (1 for each week of the school year.) In each hanging file are our 3 folders. I didn't want them in open file crates due to the dust they would collect over the course of the year, so mine are in file totes with lids. Each tote holds 6 weeks of files, plus two monthly seasonal folders.
For work like First Language Lessons and All About Spelling, which I couldn't really rip apart to file, I printed a progress sheet and attached stickers for them to use as we complete each lesson.
For any lessons where another weeks' lesson is printed on the back I attached a small post-it reminder to move it to the next weeks' folder.
Please ignore the very wrinkled tablecloth in the pictures! I've finally relaxed my laundry standards and have started letting the boys help me fold. ;-)