Some Yu-Gi-Oh cards that are worth a lot of money include The Dark Armed Dragon secret rare, which has sold for $300. The Judgment Dragon secret rare card and the Mechanical Chaser ultra rare have sold for $250 apiece as of 2015.
The Mecha Phantom Beast Draccossack secret rare card and the Tour Guide from the Underworld secret rare both sold for $200 in past exchanges. Nekroz of Brionac secret rare and Pot of Duality both sell for $150 as of 2015.
Typically cards with powerful abilities that can end duels quickly sell for higher prices because competing for money in card duels has become very popular, so whatever is spent is usually earned back quickly. Typical rare cards with special abilities to assist in winning duels max out at selling for $70 to $90.
Other cards sell for high prices due to limited production. With the Yu-Gi-Oh trading card game beginning in 1996, many cards, special or not, began circulating that were considered a must have, so production became limited to up the rarity. Some of these rare cards have been banned in tournaments, though, due to the unfair advantage they give, in order to assist more minor players.