am I gaining anything by leaving it all in the boxes? The boxes smell awful (I think a cat peed on boxes)

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IDK about you but if the boxes are saturated in urine and who knows what else, I would say to toss them. If you really care then find some of identical size and use the original styrofoam or something, just for the sake of any future transportation. *shrug*

and will keeping the computer in the plastic make it that much more valuable in the long run (i.e. capacitors/batteries leaking, etc.)?

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Keeping things in unopened plastic means you cannot check for leaking capacitors or batteries(or dead bugs and mice), and those caps could be leaking despite the machine never being used.

I picked up a 9600 brand in the box last year for $60, and had planned on keeping it mint in box...but slowly realizing that is absolutely no fun, I want them on display and running.

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IMO as long as you keep the machine and the boxes in good shape, you are doing no wrong.As far as I see things in the long run a lightly used but maintained machine in good condition is worth more than that machine that was never opened and is wrecked from it's own capacitors. But then I am no "proper" collector and someone will likely spout garbage more extreme than the garbage I just spouted.

Of course the unopened machine has more potential worth because some silly people presume that it is going to be perfect.. and they are dumb as far as I am concerned.