I always laugh when I see the 'Rare Super Mario Bros / Duck Hunt for NES' selling for $0.49 (it has to be the most numerous NES cart produced but people still call it rare on eBay).
The best way to see the value is to look at eBay's completed auctions and order them by final bid value - the games that have sold for the highest prices are generally the rarest. Things like Radiant Silvergun on Sega Saturn (regularly sells for over $200, Panzer Dragoon Saga also on Sega Saturn, Wild Gunman on NES (one just sold for $550).
I cannot think of any Amiga games that fetch these high prices though. Even though the Amiga game may be rarer (especially the later Amiga games post-1997, as they were often only selling a few hundred copies) the demand isn't there to push up the prices.