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For newer Transformers, I will keep card backs and the back panels of opened box items. For exclusives, I try to keep all of the packaging as well but it depends on the item. Some are MOC/MIB, while some are MOSC/MISB. For older toys, I try to preserve whatever packaging I have for them.

As for any other lines I collect, I will rarely keep any packaging. Joes would probably be the only exception, though it is for the bio cards. Those I clip out and file away.

I actually have about 5 boxes that only contain card backs, instruction manuals and packaging inserts. Thankfully, I'm still a long way from running out of space at our apartment by doing it this way.