I kept mine. I'm kind of a paperwork nut though. I've got a box dedicted just to things I've cut off of toy packages as well as any inserts, instructions, catalogues, mini comics--basically anything I thought was kinda neat. I think the stuff in that box goes all the way back to the late eighties.
As for my filecards, they're bagged with the figures. Except for the 25th cards of course. I kept those cardbacks intact, just as I will for the ROC toys, because I like the artwork. I do throw out the big packaging though, making certain to clip any filecards.
Guess I took the "Clip and Save for your GiJoe Command Files" thing a little too seriously.

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I don't know half of you half as well as I should like; and I like less than half of you half as well as you deserve.