Collection: NES
Many games in my NES collection are missing manuals and boxes, because most of them were bought by my dad who questioned why I "wanted to keep the packaging".
The only games that we had the boxes for were TMNT2 and Probotector (with the Konami code written down on the inside flap as is appropriate), Ironsword, Super Mario Bros. 1 and Robo Warrior. The boxes for TMNT2 and Probotector ended up getting lost while moving house, my original copy of SMB1 ended up getting stolen, and my cartridge for Ironsword ended up disappearing (not stolen by the same guy) but I still had the box.
As such, it's easy to see which games were bought later (or re-purchased). Out of the "complete" games all boxes are in great condition except for Robo Warrior, which is in really poor condition.