Basically the games I traded in during the Gamecube era. I was trading in N64, Game Boy and Gamecube games, some of which are hard to get hold of now. Most of them I've managed to replace but it will always irritate me that I've ended up with someone else's second hand copy when I had an original one which I'd owned from new.
Of the Gamecube games I sold, Four Swords adventure irks me most. I own it again now but not the big box version and the prices for that have skyrocketed. Skies of Arcadia Legends and Ikargua are two others as well, although I've seen repurchased both of them.
Another big one is Pokemon Red, the first Pokemon game I bought and I had the game, box, manual all in excellent condition. I may still have the box and manual somewhere but the game is definitely gone. I still have Blue (and got rid of Red because I didn't think it was worth keeping both) but as daft as it sounds given they're basically the same game it doesn't hold the same value for me.
On the plus side, best one I ever did was a trade with someone at school. I traded him Clayfighter for the N64 and he gave me Conkers BFD. Still got it to this day.