Use a "permanent" marker meant for writing on CDs on the containers directly. When storage is over, clean the writing with isopropyl alcohol. 

The idea is similar to moscafj's, but unlike a nonpermanent marker, it won't smudge when you hold the boxes and move them around. 

**Update** If you are uncomfortable using isopropyl alcohol, Pete Kirkham suggests in comments that dish soap plus elbow grease are sufficient to remove this kind of pen from a plastic box.