I have a copy of The Neverhood with box and manual and disk in practically mint condition. I love that game, though, only adventure game I've ever enjoyed, so I'll never end up selling it xD.
I also discovered that my copy of Star Trek Armada II with manual commands a price of over $90. That was a pleasant shock to me considering I haven't played that game since 2002 or something.
Oh, and the Half-Life 1 Anthology, which I think goes from $50 to $70 online, I managed to find for about $15 at a Half-Price Books. Can't resell though, so not that impressive (and a glitch-fest to boot).
Then I have Final Fantasy VII, with no manual, and I'll most likely not sell that. Not sure what my old N64 carts sell for - the nostalgia on those practically bans me from trying to sell them anyway, and none of them are particularly elusive.