When my olders were young we had a LOT of papers, projects, crafts, and so on that I stored. Through the years I finally hit upon a system that really worked for my brain type, our chaotic schedule, and chronic illness that didn't always allow for a tightly organized home.
1. As they finished projects or brought things home from co-ops they were stored in these wonderful plastic drawers. They worked for us because they were big enough for the bigger size of manila or construction paper. They also fit inside a closet under the lowest shelf - although I had to raise the shelf a little and took off the wheels of the cart. Each child had their own drawer with their name on the front of their drawer. Since we had 3 children storing items at the time it was perfect :).
2. At the end of each school year we would spread everything out and take pictures of each child with their projects. Then, selected items would go into a binder and the rest would go in the trash.
Admittedly, there were summers when this didn't get done. When that happened I would put a large manila paper in the drawer with a note written on it to divide the years.
Hope this helps in your organization endeavors!