Honestly, these days, the game is often the cheapest component of a package. In looking for a copy of a rare Super Famicom game, I came across a seller who had three copies available. The game by itself was £219, the game with the box was £789, and the game with the box and manual was £1199.
The logic seems to be that the box is more easily lost or damaged, so it is rarer and therefore more valuable. I'm not saying I agree with it, but that's what the market says. In the Turbo world, a loose Magical Chase was sold on eBay a few weeks ago for just under $1500. A complete copy sold a little after that for $5600.