Best of the Best, Clu Clu Land, Color A Dinosaur, Cowboy Kid, Donkey Kong Jr. Math, Fisher Price Firehouse Rescue, Gun+Nac, Panic Restaurant, Pro Sport Hockey, Sqoon, Urban Champion, Wayne's World
These are very rare boxes but not necessarily worth that much. You could probably buy these loose boxes for about the same price as a Contra cart.

Then there's the obvious ones like Stadium Events, Flintstones 2, Snow Brothers, Bonk's Adventure, etc. that are rare and DO command a high price. Recently Chubby Cherub has come into this category, but it used to be a sleeper.