In terms of rarity, the rarest games I own are games published online in small quantities from publishers such as Limited Run, Super Rare, Special Reserves, and the like.
On the other hand, value is something different. Since my collection largely focuses from the fifth generation onward, I don't have many games of high value in my personal collection, but I have a few. Valkryie Profile (PS, ~$100-$160), Haunting Ground (PS2, ~$150-$220), Lovers In A Dangerous Spacetime (NS, ~$230-$285), and Rule of Rose (PS2, ~$250-$320), namely. Prices are based on recent completed eBay listings.