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It varies with my collection, depending on several factors.

For Transformers, I will always try to keep the bio & stats section of the packaging. Sometimes that means one cut-out bit, sometimes the whole cardback or side of the box. This comes from way back in the day when they had Tech Specs cards on the back of the box/card (Clip and Save!). And sometimes the packaging design does not make this very easy (see DOTM, for example). I still have a whole box full of empty boxes waiting to be broken down because of this. F'n OCD.

For just about everything else, I'll keep cardbacks (most of the time) but any boxes get thrown away unless they're for Con/store exclusives, high-end toys (imports, 3rd Party and MPs), and/or they have resealable packaging. For example, I keep the boxes for my SDCC Soundwave, TRU Soundwave, Shinken Red Figuart and all of my TF Masterpiece toys (both domestic and imported).

I used to keep everything, but I've tried really hard to break some of those habits over the years. Attempting to move helps a lot with that, especially when you realise just how much crap you have to pack up.