My collection is part-MISB, part loose figures - roughly split 60/40 that way.

If it's been opened, I'll throw the packaging out as I don't see a point in having un-necessary clutter laying around - I may however cut the back of the box out or keep the cardback if it's a carded figure.

I don't collect G1, but if I did, they would be the exception to the rule since they're somewhat 'vintage' and I think it would be worthwhile hanging onto the packaging as they're getting increasingly harder to track down in mint condition.

G1 aside, I doubt anyone would pay a slight premium for a re-boxed used toy over a loose one (if or when you decide to sell it) anyway.