Its simple. The 'classic' Nintendo games are more expensive because people want to own them in their original version. That's why you will find people paying $40-50 US for a boxed copy of Link to the Past or $60-80 for a boxed copy of Super Metroid. Its not that they're harder to find than other games. Its because they're in more demand.
Frankly, with the deal you get with Virtual Console on the Wii, people should be less picky. 8 bucks for SNES games and 5 bucks for NES games, you'll never be able to match that on Ebay. Not that I want people to change as I sell games on Ebay and I've made quite a lot of money off peoples desire to buy $50 dollar used Dragon Warrior carts or $20 copies of Legend of Zelda.